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Ousalem F, Ngo S, Oïffer T, Omairi-Nasser A, Hamon M, Monlezun L, Boël G. Global regulation via modulation of ribosome pausing by the ABC-F protein EttA. Nat Commun 2024; 15:6314. [PMID: 39060293 PMCID: PMC11282234 DOI: 10.1038/s41467-024-50627-z] [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: 01/26/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Having multiple rounds of translation of the same mRNA creates dynamic complexities along with opportunities for regulation related to ribosome pausing and stalling at specific sequences. Yet, mechanisms controlling these critical processes and the principles guiding their evolution remain poorly understood. Through genetic, genomic, physiological, and biochemical approaches, we demonstrate that regulating ribosome pausing at specific amino acid sequences can produce ~2-fold changes in protein expression levels which strongly influence cell growth and therefore evolutionary fitness. We demonstrate, both in vivo and in vitro, that the ABC-F protein EttA directly controls the translation of mRNAs coding for a subset of enzymes in the tricarboxylic acid (TCA) cycle and its glyoxylate shunt, which modulates growth in some chemical environments. EttA also modulates expression of specific proteins involved in metabolically related physiological and stress-response pathways. These regulatory activities are mediated by EttA rescuing ribosomes paused at specific patterns of negatively charged residues within the first 30 amino acids of nascent proteins. We thus establish a unique global regulatory paradigm based on sequence-specific modulation of translational pausing.
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Affiliation(s)
- Farès Ousalem
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
- Biomarqueurs et nouvelles cibles thérapeutiques en oncologie, INSERM U981, Université Paris Saclay, Institut de Cancérologie Gustave Roussy, Villejuif Cedex, France
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Thomas Oïffer
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Amin Omairi-Nasser
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Marion Hamon
- CNRS, Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FR550, Paris, France
| | - Laura Monlezun
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.
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2
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Boyer JA, Sharma M, Dorso MA, Mai N, Amor C, Reiter JM, Kannan R, Gadal S, Xu J, Miele M, Li Z, Chen X, Chang Q, Pareja F, Worland S, Warner D, Sperry S, Chiang GG, Thompson PA, Yang G, Ouerfelli O, de Stanchina E, Wendel HG, Rosen EY, Chandarlapaty S, Rosen N. eIF4A controls translation of estrogen receptor alpha and is a therapeutic target in advanced breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593195. [PMID: 38766126 PMCID: PMC11100762 DOI: 10.1101/2024.05.08.593195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The majority of human breast cancers are dependent on hormone-stimulated estrogen receptor alpha (ER) and are sensitive to its inhibition. Treatment resistance arises in most advanced cancers due to genetic alterations that promote ligand independent activation of ER itself or ER target genes. Whereas re-targeting of the ER ligand binding domain (LBD) with newer ER antagonists can work in some cases, these drugs are largely ineffective in many genetic backgrounds including ER fusions that lose the LBD or in cancers that hyperactivate ER targets. By identifying the mechanism of ER translation, we herein present an alternative strategy to target ER and difficult to treat ER variants. We find that ER translation is cap-independent and mTOR inhibitor insensitive, but dependent on 5' UTR elements and sensitive to pharmacologic inhibition of the translation initiation factor eIF4A, an mRNA helicase. EIF4A inhibition rapidly reduces expression of ER and short-lived targets of ER such as cyclin D1 and other components of the cyclin D-CDK complex in breast cancer cells. These effects translate into suppression of growth of a variety of ligand-independent breast cancer models including those driven by ER fusion proteins that lack the ligand binding site. The efficacy of eIF4A inhibition is enhanced when it is combined with fulvestrant-an ER degrader. Concomitant inhibition of ER synthesis and induction of its degradation causes synergistic and durable inhibition of ER expression and tumor growth. The clinical importance of these findings is confirmed by results of an early clinical trial (NCT04092673) of the selective eIF4A inhibitor zotatifin in patients with estrogen receptor positive metastatic breast cancer. Multiple clinical responses have been observed on combination therapy including durable regressions. These data suggest that eIF4A inhibition could be a useful new strategy for treating advanced ER+ breast cancer.
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Affiliation(s)
- Jacob A. Boyer
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, USA
| | - Malvika Sharma
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Madeline A. Dorso
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas Mai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Corina Amor
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason M. Reiter
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Ram Kannan
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sunyana Gadal
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Jianing Xu
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Matthew Miele
- Microchemistry and Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Microchemistry and Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaoping Chen
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 11065, USA
| | - Qing Chang
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 11065, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephan Worland
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Douglas Warner
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Sam Sperry
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Gary G. Chiang
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Peggy A. Thompson
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Guangli Yang
- The Organic Synthesis Core Facility, MSK, New York, NY, USA
| | | | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 11065, USA
| | - Hans-Guido Wendel
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ezra Y. Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Neal Rosen
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
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3
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Sananmuang T, Puthier D, Nguyen C, Chokeshaiusaha K. Differential transcript usage across mammalian oocytes at the germinal vesicle and metaphase II stages. Theriogenology 2024; 215:1-9. [PMID: 37995439 DOI: 10.1016/j.theriogenology.2023.11.016] [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: 08/22/2023] [Revised: 11/11/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Ongoing progress in mRNA-Sequencing technologies has significantly contributed to the refinement of assisted reproductive technologies. However, the prior investigations have predominantly concentrated on alterations in overall gene expression levels, thereby leaving a considerable gap in our understanding of the influence of transcript isoform expression on fundamental cellular mechanisms of oocytes. Given the efficacy of differential transcript usage (DTU) analysis to address such knowledge, we conducted comprehensive DTU analysis utilizing mRNA-Seq datasets of germinal vesicle (GV) and metaphase II (MII) oocytes across six mammalian species from the SRA database, including cow, donkey, horse, human, mouse, and pig. To further illuminate the roles of these genes, we also conducted a rigorous Gene Ontology (GO) term enrichment analysis. While the DTU analysis of each species exhibited several genes with alterations in their transcript isoform usage, referred to as DTU genes, this study focused on only ten cross-species DTU genes sharing among a minimum of five distinct species (FDR≤0.05). These cross-species DTU genes were as follows: ABCF1, CDC6, CFAP36, CNOT10, DNM3, IWS1, NBN, NDEL1, RAD50 and ZCCHC17. GO term enrichment analysis unveiled the alignment of these cross-species DTU gene functions with RNA and cell-cycle control mechanisms across diverse mammalian species, thereby suggesting their vital roles during oocyte maturation. Further exploration of the transcript isoforms of these genes hence bore the potential to uncover novel transcript isoform markers for future reproductive technologies in both human and animal contexts.
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Affiliation(s)
- Thanida Sananmuang
- Rajamangala University of Technology Tawan-OK, Faculty of Veterinary Medicine, Chonburi, Thailand
| | - Denis Puthier
- Aix-Marseille Université, INSERM UMR 1090, TAGC, Marseille, France
| | - Catherine Nguyen
- Aix-Marseille Université, INSERM UMR 1090, TAGC, Marseille, France
| | - Kaj Chokeshaiusaha
- Rajamangala University of Technology Tawan-OK, Faculty of Veterinary Medicine, Chonburi, Thailand.
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4
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Schmidt N, Ganskih S, Wei Y, Gabel A, Zielinski S, Keshishian H, Lareau CA, Zimmermann L, Makroczyova J, Pearce C, Krey K, Hennig T, Stegmaier S, Moyon L, Horlacher M, Werner S, Aydin J, Olguin-Nava M, Potabattula R, Kibe A, Dölken L, Smyth RP, Caliskan N, Marsico A, Krempl C, Bodem J, Pichlmair A, Carr SA, Chlanda P, Erhard F, Munschauer M. SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9. Cell 2023; 186:4834-4850.e23. [PMID: 37794589 PMCID: PMC10617981 DOI: 10.1016/j.cell.2023.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 07/13/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Regulation of viral RNA biogenesis is fundamental to productive SARS-CoV-2 infection. To characterize host RNA-binding proteins (RBPs) involved in this process, we biochemically identified proteins bound to genomic and subgenomic SARS-CoV-2 RNAs. We find that the host protein SND1 binds the 5' end of negative-sense viral RNA and is required for SARS-CoV-2 RNA synthesis. SND1-depleted cells form smaller replication organelles and display diminished virus growth kinetics. We discover that NSP9, a viral RBP and direct SND1 interaction partner, is covalently linked to the 5' ends of positive- and negative-sense RNAs produced during infection. These linkages occur at replication-transcription initiation sites, consistent with NSP9 priming viral RNA synthesis. Mechanistically, SND1 remodels NSP9 occupancy and alters the covalent linkage of NSP9 to initiating nucleotides in viral RNA. Our findings implicate NSP9 in the initiation of SARS-CoV-2 RNA synthesis and unravel an unsuspected role of a cellular protein in orchestrating viral RNA production.
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Affiliation(s)
- Nora Schmidt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Yuanjie Wei
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Alexander Gabel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Sebastian Zielinski
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | | | - Caleb A Lareau
- Program in Computational and System Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liv Zimmermann
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jana Makroczyova
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Karsten Krey
- School of Medicine, Institute of Virology, Technical University of Munich, Munich, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Sebastian Stegmaier
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lambert Moyon
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Marc Horlacher
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Simone Werner
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Jens Aydin
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Marco Olguin-Nava
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Ramya Potabattula
- Institute of Human Genetics, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Anuja Kibe
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Christine Krempl
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Jochen Bodem
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Andreas Pichlmair
- School of Medicine, Institute of Virology, Technical University of Munich, Munich, Germany; German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Petr Chlanda
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany; Faculty for Computer and Data Science, University of Regensburg, Regensburg, Germany
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany; Faculty of Medicine, Julius-Maximilians-University Würzburg, Würzburg, Germany.
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5
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Cao QT, Ishak M, Shpilman I, Hirota JA. TNF-α and Poly(I:C) induction of A20 and activation of NF-κB signaling are independent of ABCF1 in human airway epithelial cells. Sci Rep 2023; 13:14745. [PMID: 37679460 PMCID: PMC10485056 DOI: 10.1038/s41598-023-41990-w] [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: 12/22/2022] [Accepted: 09/04/2023] [Indexed: 09/09/2023] Open
Abstract
ABCF1 is the most characterized member of the ABCF family in eukaryotes with proposed functions related to innate immunity in fibroblasts, macrophages, and epithelial cells. Currently, a mechanistic link between ABCF1 and immune responses in human airway epithelial cells (HAECs) remains to be clearly defined. The present study aimed at characterizing the function of ABCF1 in the context of nuclear factor nuclear factor κB (NF-κB) mediated pro-inflammatory responses in an immortalized human airway epithelial cell line, HBEC-6KT. We demonstrated that with ABCF1 silencing under basal conditions, TNF Alpha Induced Protein 3 (TNFAIP3/A20) protein expression and downstream expression and activation of transcription factors, NF-κB and Interferon regulatory factor 3 (IRF-3), were not disrupted. We followed with investigations of ABCF1 function under a pro-inflammatory stimuli that are known to be regulated by A20. We demonstrated that under Polyinosinic:polycytidylic acid (Poly(I:C)) and tumor Necrosis Factor-α (TNF-α) challenge with ABCF1 silencing, there was a significant reduction in secreted levels of interleukin-8 (IL-8) and a trend for reduced IL-6. However, we observed no changes to the expression levels of A20 and the activation status of the transcription factors, NF-κB and IRF-3. Collectively, these studies demonstrate that Poly(I:C) and TNF-α induced IL-8 is regulated by ABCF1 via pathways independent of NF-κB and IRF-3 activation.
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Affiliation(s)
- Quynh T Cao
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, L8N 4A6, Canada
| | - Mira Ishak
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, L8N 4A6, Canada
| | - Israel Shpilman
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, L8N 4A6, Canada
| | - Jeremy A Hirota
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, L8N 4A6, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, V6H 3Z6, Canada.
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6
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Govande AA, Babnis AW, Urban C, Habjan M, Hartmann R, Kranzusch PJ, Pichlmair A. RNase L-activating 2'-5' oligoadenylates bind ABCF1, ABCF3 and Decr-1. J Gen Virol 2023; 104. [PMID: 37676257 DOI: 10.1099/jgv.0.001890] [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] [Indexed: 09/08/2023] Open
Abstract
A notable signalling mechanism employed by mammalian innate immune signalling pathways uses nucleotide-based second messengers such as 2'3'-cGAMP and 2'-5'-oligoadenylates (OAs), which bind and activate STING and RNase L, respectively. Interestingly, the involvement of nucleotide second messengers to activate antiviral responses is evolutionarily conserved, as evidenced by the identification of an antiviral cGAMP-dependent pathway in Drosophila. Using a mass spectrometry approach, we identified several members of the ABCF family in human, mouse and Drosophila cell lysates as 2'-5' OA-binding proteins, suggesting an evolutionarily conserved function. Biochemical characterization of these interactions demonstrates high-affinity binding of 2'-5' OA to ABCF1, dependent on phosphorylated 2'-5' OA and an intact Walker A/B motif of the ABC cassette of ABCF1. As further support for species-specific interactions with 2'-5' OA, we additionally identified that the metabolic enzyme Decr1 from mouse, but not human or Drosophila cells, forms a high-affinity complex with 2'-5' OA. A 1.4 Å co-crystal structure of the mouse Decr1-2'-5' OA complex explains high-affinity recognition of 2'-5' OA and the mechanism of species specificity. Despite clear evidence of physical interactions, we could not identify profound antiviral functions of ABCF1, ABCF3 or Decr1 or 2'-5' OA-dependent regulation of cellular translation rates, as suggested by the engagement of ABCF proteins. Thus, although the biological consequences of the here identified interactions need to be further studied, our data suggest that 2'-5' OA can serve as a signalling hub to distribute a signal to different recipient proteins.
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Affiliation(s)
- Apurva A Govande
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Christian Urban
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Matthias Habjan
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Rune Hartmann
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Andreas Pichlmair
- Institute of Virology, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany
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7
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Ousalem F, Singh S, Bailey NA, Wong KH, Zhu L, Neky MJ, Sibindi C, Fei J, Gonzalez RL, Boël G, Hunt JF. Comparative genetic, biochemical, and biophysical analyses of the four E. coli ABCF paralogs support distinct functions related to mRNA translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.543863. [PMID: 37398404 PMCID: PMC10312648 DOI: 10.1101/2023.06.11.543863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Multiple paralogous ABCF ATPases are encoded in most genomes, but the physiological functions remain unknown for most of them. We herein compare the four Escherichia coli K12 ABCFs - EttA, Uup, YbiT, and YheS - using assays previously employed to demonstrate EttA gates the first step of polypeptide elongation on the ribosome dependent on ATP/ADP ratio. A Δ uup knockout, like Δ ettA , exhibits strongly reduced fitness when growth is restarted from long-term stationary phase, but neither Δ ybiT nor Δ yheS exhibits this phenotype. All four proteins nonetheless functionally interact with ribosomes based on in vitro translation and single-molecule fluorescence resonance energy transfer experiments employing variants harboring glutamate-to-glutamine active-site mutations (EQ 2 ) that trap them in the ATP-bound conformation. These variants all strongly stabilize the same global conformational state of a ribosomal elongation complex harboring deacylated tRNA Val in the P site. However, EQ 2 -Uup uniquely exchanges on/off the ribosome on a second timescale, while EQ 2 -YheS-bound ribosomes uniquely sample alternative global conformations. At sub-micromolar concentrations, EQ 2 -EttA and EQ 2 -YbiT fully inhibit in vitro translation of an mRNA encoding luciferase, while EQ 2 -Uup and EQ 2 -YheS only partially inhibit it at ~10-fold higher concentrations. Moreover, tripeptide synthesis reactions are not inhibited by EQ 2 -Uup or EQ 2 -YheS, while EQ 2 -YbiT inhibits synthesis of both peptide bonds and EQ 2 -EttA specifically traps ribosomes after synthesis of the first peptide bond. These results support the four E. coli ABCF paralogs all having different activities on translating ribosomes, and they suggest that there remains a substantial amount of functionally uncharacterized "dark matter" involved in mRNA translation.
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8
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Turner M. Regulation and function of poised mRNAs in lymphocytes. Bioessays 2023; 45:e2200236. [PMID: 37009769 DOI: 10.1002/bies.202200236] [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: 12/07/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 04/04/2023]
Abstract
Pre-existing but untranslated or 'poised' mRNA exists as a means to rapidly induce the production of specific proteins in response to stimuli and as a safeguard to limit the actions of these proteins. The translation of poised mRNA enables immune cells to express quickly genes that enhance immune responses. The molecular mechanisms that repress the translation of poised mRNA and, upon stimulation, enable translation have yet to be elucidated. They likely reflect intrinsic properties of the mRNAs and their interactions with trans-acting factors that direct poised mRNAs away from or into the ribosome. Here, I discuss mechanisms by which this might be regulated.
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Affiliation(s)
- Martin Turner
- Immunology Programme, The Babraham Institute, Cambridge, UK
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9
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Fan J, Ding Y, Huang H, Xiong S, He L, Guo J. High expression of ABCF1 is an independent predictor of poor prognosis in bladder cancer. BMC Urol 2023; 23:37. [PMID: 36932399 PMCID: PMC10022215 DOI: 10.1186/s12894-023-01211-y] [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: 12/03/2022] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
ABCF1, a member of the ATP-binding cassette (ABC) transporter family, is involved in the malignant progression of tumors. However, the role of ABCF1 in bladder cancer is poorly understood. In our study, we explored the differential expression of ABCF1 in bladder cancer and normal bladder tissues based on bioinformatic analysis and immunohistochemical results. GSEA was performed to ascertain the potential related signaling pathways of ABCF1. The relationship between ABCF1 expression and bladder cancer progression was analyzed using the GSE13507 dataset. In addition, the differential expression of ABCF1 in the cell lines was verified by quantitative real-time polymerase chain reaction (qRT‒PCR) and Western blotting. ABCF1 was upregulated in bladder cancer, and the high expression of ABCF1 was closely related to sex (P = 0.00056), grade (P = 0.00049), T stage (P = 0.00007), and N stage (P = 0.0076). High expression of ABCF1 was correlated with poor overall survival in bladder cancer patients (P < 0.001). In addition, univariate and multivariate Cox regression analyses showed that high ABCF1 expression was an independent factor for poor prognosis in bladder cancer patients. Therefore, ABCF1 expression is closely related to the progression of bladder cancer and can be used as a potential indicator of poor prognosis and a therapeutic target for bladder cancer.
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Affiliation(s)
- JiaWen Fan
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yi Ding
- The Second Affiliated Hospital of Jiujiang University, Jiujiang, Jiangxi, China
| | - HaoXuan Huang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - ShiDa Xiong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Liang He
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Ju Guo
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.
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10
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Yang Y, Lu K, Qian J, Guo J, Xu H, Lu Z. Identification and characterization of ABC proteins in an important rice insect pest, Cnaphalocrocis medinalis unveil their response to Cry1C toxin. Int J Biol Macromol 2023; 237:123949. [PMID: 36894061 DOI: 10.1016/j.ijbiomac.2023.123949] [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: 08/12/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023]
Abstract
Rice leaffolder (Cnaphalocrocis medinalis) is an important insect pest in paddy fields. Due to their essential role in the physiology and insecticidal resistance, ATP-binding cassette (ABC) proteins were studied in many insects. In this study, we identified the ABC proteins in C. medinalis through genomic data and analyzed their molecular characteristics. A total of 37 sequences with nucleotide-binding domain (NBD) were identified as ABC proteins and belonged to eight families (ABCA-ABCH). Four structure styles of ABC proteins were found in C. medinalis, including full structure, half structure, single structure, and ABC2 structure. In addition to these structures, TMD-NBD-TMD, NBD-TMD-NBD, and NBD-TMD-NBD-NBD were found in C. medinalis ABC proteins. Docking studies suggested that in addition to the soluble ABC proteins, other ABC proteins including ABCC4, ABCH1, ABCG3, ABCB5, ABCG1, ABCC7, ABCB3, ABCA3, and ABCC5 binding with Cry1C had higher weighted scores. The upregulation of ABCB1 and downregulation of ABCB3, ABCC1, ABCC7, ABCG1, ABCG3, and ABCG6 were associated with the C. medinalis response to Cry1C toxin. Collectively, these results help elucidate the molecular characteristics of C. medinalis ABC proteins, pave the way for further functional studies of C. medinalis ABC proteins, including their interaction with Cry1C toxin, and provide potential insecticide targets.
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Affiliation(s)
- Yajun Yang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China
| | - Ke Lu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China; Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianing Qian
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China
| | - Jiawen Guo
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China
| | - Hongxing Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China.
| | - Zhongxian Lu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China.
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11
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Shi W, Hu R, Zhao R, Zhu J, Shen H, Li H, Wang L, Yang Z, Jiang Q, Qiao Y, Jiang G, Cheng J, Wan X. Transcriptome analysis of hepatopancreas and gills of Palaemon gravieri under salinity stress. Gene 2022; 851:147013. [DOI: 10.1016/j.gene.2022.147013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/01/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
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12
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Multiple Roles of m6A RNA Modification in Translational Regulation in Cancer. Int J Mol Sci 2022; 23:ijms23168971. [PMID: 36012237 PMCID: PMC9408962 DOI: 10.3390/ijms23168971] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Despite its discovery in the early 1970s, m6A modification within mRNA molecules has only powerfully entered the oncology field in recent years. This chemical modification can control all aspects of the maturation of mRNAs, both in the nucleus and in the cytoplasm. Thus, the alteration in expression levels of writers, erasers, and readers may significantly contribute to the alteration of gene expression observed in cancer. In particular, the activation of oncogenic pathways can lead to an alteration of the global rate of mRNA translation or the selective translation of specific mRNAs. In both cases, m6A can play an important role. In this review, we highlight the role of m6A in the regulation of translation by focusing on regulatory mechanisms and cancer-related functions of this novel but still controversial field.
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13
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Abstract
Enterovirus 71 (EV71) is the major pathogen of hand, foot, and mouth disease. In severe cases, it can cause life-threatening neurological complications, such as aseptic meningitis and polio-like paralysis. There are no specific antiviral treatments for EV71 infections. In a previous study, the host protein growth arrest and DNA damage-inducible protein 34 (GADD34) expression was upregulated during EV71 infection determined by ribosome profiling and RNA-sequencing. Here, we investigated the interactions of host protein GADD34 and EV71 during infections. Rhabdomyosarcoma (RD) cells were infected with EV71 resulting in a significant increase in expression of GADD34 mRNA and protein. Through screening of EV71 protein we determined that the non-structural precursor protein 3CD is responsible for upregulating GADD34. EV71 3CD increased the RNA and protein levels of GADD34, while the 3CD mutant Y441S could not. 3CD upregulated GADD34 translation via the upstream open reading frame (uORF) of GADD34 5'untranslated regions (UTR). EV71 replication was attenuated by the knockdown of GADD34. The function of GADD34 to dephosphorylate eIF2α was unrelated to the upregulation of EV71 replication, but the PEST 1, 2, and 3 regions of GADD34 were required. GADD34 promoted the EV71 internal ribosome entry site (IRES) activity through the PEST repeats and affected several other viruses. Finally, GADD34 amino acids 563 to 565 interacted with 3CD, assisting GADD34 to target the EV71 IRES. Our research reveals a new mechanism by which GADD34 promotes viral IRES and how the EV71 non-structural precursor protein 3CD regulates host protein expression to support viral replication. IMPORTANCE Identification of host factors involved in viral replication is an important approach in discovering viral pathogenic mechanisms and identifying potential therapeutic targets. Previously, we screened host proteins that were upregulated by EV71 infection. Here, we report the interaction between the upregulated host protein GADD34 and EV71. EV71 non-structural precursor protein 3CD activates the RNA and protein expression of GADD34. Our study reveals that 3CD regulates the uORF of the 5′-UTR to increase GADD34 translation, providing a new explanation for how viral proteins regulate host protein expression. GADD34 is important for EV71 replication, and the key functional domains of GADD34 that promote EV71 are PEST 1, 2, and 3 regions. We report that GADD34 promotes viral IRES for the first time and this process is independent of its eIF2α phosphatase activity.
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14
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Cui Z, Li X, Shin J, Gamper H, Hou YM, Sacchettini JC, Zhang J. Interplay between an ATP-binding cassette F protein and the ribosome from Mycobacterium tuberculosis. Nat Commun 2022; 13:432. [PMID: 35064151 PMCID: PMC8782954 DOI: 10.1038/s41467-022-28078-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/07/2022] [Indexed: 12/22/2022] Open
Abstract
EttA, energy-dependent translational throttle A, is a ribosomal factor that gates ribosome entry into the translation elongation cycle. A detailed understanding of its mechanism of action is limited due to the lack of high-resolution structures along its ATPase cycle. Here we present the cryo-electron microscopy (cryo-EM) structures of EttA from Mycobacterium tuberculosis (Mtb), referred to as MtbEttA, in complex with the Mtb 70S ribosome initiation complex (70SIC) at the pre-hydrolysis (ADPNP) and transition (ADP-VO4) states, and the crystal structure of MtbEttA alone in the post-hydrolysis (ADP) state. We observe that MtbEttA binds the E-site of the Mtb 70SIC, remodeling the P-site tRNA and the ribosomal intersubunit bridge B7a during the ribosomal ratcheting. In return, the rotation of the 30S causes conformational changes in MtbEttA, forcing the two nucleotide-binding sites (NBSs) to alternate to engage each ADPNP in the pre-hydrolysis states, followed by complete engagements of both ADP-VO4 molecules in the ATP-hydrolysis transition states. In the post-hydrolysis state, the conserved ATP-hydrolysis motifs of MtbEttA dissociate from both ADP molecules, leaving two nucleotide-binding domains (NBDs) in an open conformation. These structures reveal a dynamic interplay between MtbEttA and the Mtb ribosome, providing insights into the mechanism of translational regulation by EttA-like proteins.
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Affiliation(s)
- Zhicheng Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Xiaojun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Joonyoung Shin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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15
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Choi EB, Vodnala M, Zerbato M, Wang J, Ho JJ, Inouye C, Ding L, Fong YW. ATP-binding cassette protein ABCF1 couples transcription and genome surveillance in embryonic stem cells through low-complexity domain. SCIENCE ADVANCES 2021; 7:eabk2775. [PMID: 34714667 PMCID: PMC8555894 DOI: 10.1126/sciadv.abk2775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
OCT4 and SOX2 confer pluripotency by recruiting coactivators to activate stem cell–specific transcription. However, the composition of coactivator complexes and their roles in maintaining stem cell fidelity remain unclear. Here, we report the ATP-binding cassette subfamily F member 1 (ABCF1) as a coactivator for OCT4/SOX2 critical for stem cell self-renewal. The intrinsically disordered low-complexity domain (LCD) of ABCF1 contributes to phase separation in vitro and transcriptional activation of pluripotency genes by mediating multivalent interactions with SOX2 and co-dependent coactivators XPC and DKC1. These LCD-driven transcription factor–coactivator interactions critical for pluripotency gene expression are disrupted by DNA damage, likely due to LCD-dependent binding of ABCF1 to damage-generated intracellular DNA fragments instead of SOX2. This study identifies a transcriptional coactivator that uses its LCD to form selective multivalent interactions to regulate stem cell self-renewal and exit from pluripotency when genome integrity is compromised.
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Affiliation(s)
- Eun-Bee Choi
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Munender Vodnala
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Madeleine Zerbato
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jianing Wang
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jaclyn J. Ho
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Carla Inouye
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Lai Ding
- Department of Neurology, Program for Interdisciplinary Neuroscience, Brigham and Women’s Hospital, Boston, MA, USA
| | - Yick W. Fong
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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16
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Serra M, Hattinger CM, Pasello M, Casotti C, Fantoni L, Riganti C, Manara MC. Impact of ABC Transporters in Osteosarcoma and Ewing's Sarcoma: Which Are Involved in Chemoresistance and Which Are Not? Cells 2021; 10:cells10092461. [PMID: 34572110 PMCID: PMC8467338 DOI: 10.3390/cells10092461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/16/2022] Open
Abstract
The ATP-binding cassette (ABC) transporter superfamily consists of several proteins with a wide repertoire of functions. Under physiological conditions, ABC transporters are involved in cellular trafficking of hormones, lipids, ions, xenobiotics, and several other molecules, including a broad spectrum of chemical substrates and chemotherapeutic drugs. In cancers, ABC transporters have been intensely studied over the past decades, mostly for their involvement in the multidrug resistance (MDR) phenotype. This review provides an overview of ABC transporters, both related and unrelated to MDR, which have been studied in osteosarcoma and Ewing's sarcoma. Since different backbone drugs used in first-line or rescue chemotherapy for these two rare bone sarcomas are substrates of ABC transporters, this review particularly focused on studies that have provided findings that have been either translated to clinical practice or have indicated new candidate therapeutic targets; however, findings obtained from ABC transporters that were not directly involved in drug resistance were also discussed, in order to provide a more complete overview of the biological impacts of these molecules in osteosarcoma and Ewing's sarcoma. Finally, therapeutic strategies and agents aimed to circumvent ABC-mediated chemoresistance were discussed to provide future perspectives about possible treatment improvements of these neoplasms.
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Affiliation(s)
- Massimo Serra
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
- Correspondence: ; Tel.: +39-051-6366762
| | - Claudia Maria Hattinger
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
| | - Michela Pasello
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
| | - Chiara Casotti
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
| | - Leonardo Fantoni
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
| | - Chiara Riganti
- Department of Oncology, University of Torino, Via Santena 5/bis, 10126 Torino, Italy;
| | - Maria Cristina Manara
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (C.M.H.); (M.P.); (C.C.); (L.F.); (M.C.M.)
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17
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Kumar V, Garg S, Gupta L, Gupta K, Diagne CT, Missé D, Pompon J, Kumar S, Saxena V. Delineating the Role of Aedes aegypti ABC Transporter Gene Family during Mosquito Development and Arboviral Infection via Transcriptome Analyses. Pathogens 2021; 10:1127. [PMID: 34578158 PMCID: PMC8470938 DOI: 10.3390/pathogens10091127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Aedes aegypti acts as a vector for several arboviral diseases that impose a major socio-economic burden. Moreover, the absence of a vaccine against these diseases and drug resistance in mosquitoes necessitates the development of new control strategies for vector-borne diseases. ABC transporters that play a vital role in immunity and other cellular processes in different organisms may act as non-canonical immune molecules against arboviruses, however, their role in mosquito immunity remains unexplored. This study comprehensively analyzed various genetic features of putative ABC transporters and classified them into A-H subfamilies based on their evolutionary relationships. Existing RNA-sequencing data analysis indicated higher expression of cytosolic ABC transporter genes (E & F Subfamily) throughout the mosquito development, while members of other subfamilies exhibited tissue and time-specific expression. Furthermore, comparative gene expression analysis from the microarray dataset of mosquito infected with dengue, yellow fever and West Nile viruses revealed 31 commonly expressed ABC transporters suggesting a potentially conserved transcriptomic signature of arboviral infection. Among these, only a few transporters of ABCA, ABCC and ABCF subfamily were upregulated, while most were downregulated. This indicates the possible involvement of ABC transporters in mosquito immunity.
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Affiliation(s)
- Vikas Kumar
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani 333031, India or (V.K.); (S.G.)
| | - Shilpi Garg
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani 333031, India or (V.K.); (S.G.)
| | - Lalita Gupta
- Department of Zoology, Chaudhary Bansi Lal University, Bhiwani 127021, India or
| | - Kuldeep Gupta
- Department of Radiology and Radiological Sciences, School of Medicine, 470 Cancer Research Building-II, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Cheikh Tidiane Diagne
- MIVEGEC, Univ. Montpellier, IRD, CNRS, 34394 Montpellier, France; (C.T.D.); (D.M.); (J.P.)
| | - Dorothée Missé
- MIVEGEC, Univ. Montpellier, IRD, CNRS, 34394 Montpellier, France; (C.T.D.); (D.M.); (J.P.)
| | - Julien Pompon
- MIVEGEC, Univ. Montpellier, IRD, CNRS, 34394 Montpellier, France; (C.T.D.); (D.M.); (J.P.)
| | - Sanjeev Kumar
- Department of Biotechnology, Chaudhary Bansi Lal University, Bhiwani 127021, India
| | - Vishal Saxena
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani 333031, India or (V.K.); (S.G.)
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18
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Wang H, Liu S, Xun X, Li M, Lou J, Zhang Y, Shi J, Hu J, Bao Z, Hu X. Toxin- and species-dependent regulation of ATP-binding cassette (ABC) transporters in scallops after exposure to paralytic shellfish toxin-producing dinoflagellates. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 230:105697. [PMID: 33254068 DOI: 10.1016/j.aquatox.2020.105697] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
ATP-binding cassette (ABC) transporters are membrane-bound proteins involved in exporting various xenobiotic compounds from living cells. Bivalve mollusks can accumulate large amounts of paralytic shellfish toxins (PSTs) from marine dinoflagellates. For aquatic invertebrates, the importance of ABC proteins in multi-xenobiotic resistance has been demonstrated, however, the systematic identification of ABC transporters is very limited. In this study, 64 and 67 ABC genes containing all eight described subfamilies (A to H) were identified in Yesso scallop (Patinopecten yessoensis) and Zhikong scallop (Chlamys farreri), respectively, with massive gene expansion being observed in the ABCC and ABCG subfamilies. The kidney harbored more specifically expressed ABC genes than other organs/tissues, most of which belonged to ABCB, ABCC, and ABCG subfamilies. After feeding the scallops with PST-producing dinoflagellates, the expression of scallop ABC genes in the kidney was regulated in toxin- and species-dependent manners. In total, 20 and 24 ABC genes in Zhikong scallop (CfABCs) were induced after exposure to Alexandrium minutum and A. catenella, with the up-regulated members from both ABCC and ABCG subfamilies mainly showing acute and chronic induction by A. minutum and A. catenella, respectively, while the up-regulated CfABCBs mainly showing chronic induction by both dinoflagellates. In Yesso scallop, only eight ABC genes (PyABCs) were regulated after A. catenella exposure, and all the five up-regulated PyABCs were acutely induced. Our findings imply the functional diversity of scallop ABC genes in coping with PST accumulation, which may contribute to the lineage-specific adaptation of scallops for dealing with algal toxins challenge.
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Affiliation(s)
- Huizhen Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shiqi Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xiaogang Xun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Moli Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jiarun Lou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yihan Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jiaoxia Shi
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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19
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Fostier CR, Monlezun L, Ousalem F, Singh S, Hunt JF, Boël G. ABC-F translation factors: from antibiotic resistance to immune response. FEBS Lett 2020; 595:675-706. [PMID: 33135152 DOI: 10.1002/1873-3468.13984] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Energy-dependent translational throttle A (EttA) from Escherichia coli is a paradigmatic ABC-F protein that controls the first step in polypeptide elongation on the ribosome according to the cellular energy status. Biochemical and structural studies have established that ABC-F proteins generally function as translation factors that modulate the conformation of the peptidyl transferase center upon binding to the ribosomal tRNA exit site. These factors, present in both prokaryotes and eukaryotes but not in archaea, use related molecular mechanisms to modulate protein synthesis for heterogenous purposes, ranging from antibiotic resistance and rescue of stalled ribosomes to modulation of the mammalian immune response. Here, we review the canonical studies characterizing the phylogeny, regulation, ribosome interactions, and mechanisms of action of the bacterial ABC-F proteins, and discuss the implications of these studies for the molecular function of eukaryotic ABC-F proteins, including the three human family members.
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Affiliation(s)
- Corentin R Fostier
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Laura Monlezun
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Shikha Singh
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - John F Hunt
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
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20
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Cao QT, Aguiar JA, Tremblay BJM, Abbas N, Tiessen N, Revill S, Makhdami N, Ayoub A, Cox G, Ask K, Doxey AC, Hirota JA. ABCF1 Regulates dsDNA-induced Immune Responses in Human Airway Epithelial Cells. Front Cell Infect Microbiol 2020; 10:487. [PMID: 33042865 PMCID: PMC7525020 DOI: 10.3389/fcimb.2020.00487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022] Open
Abstract
Background: The airway epithelium represents a critical component of the human lung that helps orchestrate defenses against respiratory tract viral infections, which are responsible for more than 2.5 million deaths/year globally. Innate immune activities of the airway epithelium rely on Toll-like receptors (TLRs), nucleotide binding and leucine-rich-repeat pyrin domain containing (NLRP) receptors, and cytosolic nucleic acid sensors. ATP Binding Cassette (ABC) transporters are ubiquitous across all three domains of life—Archaea, Bacteria, and Eukarya—and expressed in the human airway epithelium. ABCF1, a unique ABC family member that lacks a transmembrane domain, has been defined as a cytosolic nucleic acid sensor that regulates CXCL10, interferon-β expression, and downstream type I interferon responses. We tested the hypothesis that ABCF1 functions as a dsDNA nucleic acid sensor in human airway epithelial cells important in regulating antiviral responses. Methods: Expression and localization experiments were performed using in situ hybridization and immunohistochemistry in human lung tissue, while confirmatory transcript and protein expression was performed in human airway epithelial cells. Functional experiments were performed with siRNA methods in a human airway epithelial cell line. Complementary transcriptomic analyses were performed to explore the contributions of ABCF1 to gene expression patterns. Results: Using archived human lung and human airway epithelial cells, we confirm expression of ABCF1 gene and protein expression in these tissue samples, with a role for mediating CXCL10 production in response to dsDNA viral mimic challenge. Although, ABCF1 knockdown was associated with an attenuation of select genes involved in the antiviral responses, Gene Ontology analyses revealed a greater interaction of ABCF1 with TLR signaling suggesting a multifactorial role for ABCF1 in innate immunity in human airway epithelial cells. Conclusion: ABCF1 is a candidate cytosolic nucleic acid sensor and modulator of TLR signaling that is expressed at gene and protein levels in human airway epithelial cells. The precise level where ABCF1 protein functions to modulate immune responses to pathogens remains to be determined but is anticipated to involve IRF-3 and CXCL10 production.
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Affiliation(s)
- Quynh T Cao
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, Canada
| | | | | | - Nadin Abbas
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, Canada
| | - Nicholas Tiessen
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, Canada
| | - Spencer Revill
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, Canada
| | - Nima Makhdami
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, Canada
| | - Anmar Ayoub
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, Canada
| | - Gerard Cox
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, Canada
| | - Kjetil Ask
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Andrew C Doxey
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, Canada.,Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jeremy A Hirota
- Division of Respirology, Department of Medicine, Firestone Institute for Respiratory Health, McMaster University, Hamilton, ON, Canada.,Department of Biology, University of Waterloo, Waterloo, ON, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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21
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Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020; 21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Rivka Dikstein
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
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22
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Phylogenetic analysis of the ATP-binding cassette proteins suggests a new ABC protein subfamily J in Aedes aegypti (Diptera: Culicidae). BMC Genomics 2020; 21:463. [PMID: 32631258 PMCID: PMC7339416 DOI: 10.1186/s12864-020-06873-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/26/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND We performed an in-depth analysis of the ABC gene family in Aedes aegypti (Diptera: Culicidae), which is an important vector species of arthropod-borne viral infections such as chikungunya, dengue, and Zika. Despite its importance, previous studies of the Arthropod ABC family have not focused on this species. Reports of insecticide resistance among pests and vectors indicate that some of these ATP-dependent efflux pumps are involved in compound traffic and multidrug resistance phenotypes. RESULTS We identified 53 classic complete ABC proteins annotated in the A. aegypti genome. A phylogenetic analysis of Aedes aegypti ABC proteins was carried out to assign the novel proteins to the ABC subfamilies. We also determined 9 full-length sequences of DNA repair (MutS, RAD50) and structural maintenance of chromosome (SMC) proteins that contain the ABC signature. CONCLUSIONS After inclusion of the putative ABC proteins into the evolutionary tree of the gene family, we classified A. aegypti ABC proteins into the established subfamilies (A to H), but the phylogenetic positioning of MutS, RAD50 and SMC proteins among ABC subfamilies-as well as the highly supported grouping of RAD50 and SMC-prompted us to name a new J subfamily of A. aegypti ABC proteins.
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23
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CIGB-300 anticancer peptide regulates the protein kinase CK2-dependent phosphoproteome. Mol Cell Biochem 2020; 470:63-75. [PMID: 32405972 DOI: 10.1007/s11010-020-03747-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/06/2020] [Indexed: 10/24/2022]
Abstract
Casein-kinase CK2 is a Ser/Thr protein kinase that fosters cell survival and proliferation of malignant cells. The CK2 holoenzyme, formed by the association of two catalytic alpha/alpha' (CK2α/CK2α') and two regulatory beta subunits (CK2β), phosphorylates diverse intracellular proteins partaking in key cellular processes. A handful of such CK2 substrates have been identified as targets for the substrate-binding anticancer peptide CIGB-300. However, since CK2β also contains a CK2 phosphorylation consensus motif, this peptide may also directly impinge on CK2 enzymatic activity, thus globally modifying the CK2-dependent phosphoproteome. To address such a possibility, firstly, we evaluated the potential interaction of CIGB-300 with CK2 subunits, both in cell-free assays and cellular lysates, as well as its effect on CK2 enzymatic activity. Then, we performed a phosphoproteomic survey focusing on early inhibitory events triggered by CIGB-300 and identified those CK2 substrates significantly inhibited along with disturbed cellular processes. Altogether, we provided here the first evidence for a direct impairment of CK2 enzymatic activity by CIGB-300. Of note, both CK2-mediated inhibitory mechanisms of this anticancer peptide (i.e., substrate- and enzyme-binding mechanism) may run in parallel in tumor cells and help to explain the different anti-neoplastic effects exerted by CIGB-300 in preclinical cancer models.
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24
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Sabrialabed S, Yang JG, Yariv E, Ben-Tal N, Lewinson O. Substrate recognition and ATPase activity of the E. coli cysteine/cystine ABC transporter YecSC-FliY. J Biol Chem 2020; 295:5245-5256. [PMID: 32144203 PMCID: PMC7170509 DOI: 10.1074/jbc.ra119.012063] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/03/2020] [Indexed: 12/20/2022] Open
Abstract
Sulfur is essential for biological processes such as amino acid biogenesis, iron-sulfur cluster formation, and redox homeostasis. To acquire sulfur-containing compounds from the environment, bacteria have evolved high-affinity uptake systems, predominant among which is the ABC transporter family. Theses membrane-embedded enzymes use the energy of ATP hydrolysis for transmembrane transport of a wide range of biomolecules against concentration gradients. Three distinct bacterial ABC import systems of sulfur-containing compounds have been identified, but the molecular details of their transport mechanism remain poorly characterized. Here we provide results from a biochemical analysis of the purified Escherichia coli YecSC-FliY cysteine/cystine import system. We found that the substrate-binding protein FliY binds l-cystine, l-cysteine, and d-cysteine with micromolar affinities. However, binding of the l- and d-enantiomers induced different conformational changes of FliY, where the l- enantiomer-substrate-binding protein complex interacted more efficiently with the YecSC transporter. YecSC had low basal ATPase activity that was moderately stimulated by apo FliY, more strongly by d-cysteine-bound FliY, and maximally by l-cysteine- or l-cystine-bound FliY. However, at high FliY concentrations, YecSC reached maximal ATPase rates independent of the presence or nature of the substrate. These results suggest that FliY exists in a conformational equilibrium between an open, unliganded form that does not bind to the YecSC transporter and closed, unliganded and closed, liganded forms that bind this transporter with variable affinities but equally stimulate its ATPase activity. These findings differ from previous observations for similar ABC transporters, highlighting the extent of mechanistic diversity in this large protein family.
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Affiliation(s)
- Siwar Sabrialabed
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Janet G Yang
- Department of Chemistry, University of San Francisco, San Francisco, California 94117
| | - Elon Yariv
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6139001, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6139001, Israel
| | - Oded Lewinson
- Department of Biochemistry and the Rappaport Institute for Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
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25
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Dazzoni R, Grélard A, Morvan E, Bouter A, Applebee CJ, Loquet A, Larijani B, Dufourc EJ. The unprecedented membrane deformation of the human nuclear envelope, in a magnetic field, indicates formation of nuclear membrane invaginations. Sci Rep 2020; 10:5147. [PMID: 32198481 PMCID: PMC7083927 DOI: 10.1038/s41598-020-61746-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/14/2020] [Indexed: 12/04/2022] Open
Abstract
Human nuclear membrane (hNM) invaginations are thought to be crucial in fusion, fission and remodeling of cells and present in many human diseases. There is however little knowledge, if any, about their lipid composition and dynamics. We therefore isolated nuclear envelope lipids from human kidney cells, analyzed their composition and determined the membrane dynamics after resuspension in buffer. The hNM lipid extract was composed of a complex mixture of phospholipids, with high amounts of phosphatidylcholines, phosphatidylinositols (PI) and cholesterol. hNM dynamics was determined by solid-state NMR and revealed that the lamellar gel-to-fluid phase transition occurs below 0 °C, reflecting the presence of elevated amounts of unsaturated fatty acid chains. Fluidity was higher than the plasma membrane, illustrating the dual action of Cholesterol (ordering) and PI lipids (disordering). The most striking result was the large magnetic field-induced membrane deformation allowing to determine the membrane bending elasticity, a property related to hydrodynamics of cells and organelles. Human Nuclear Lipid Membranes were at least two orders of magnitude more elastic than the classical plasma membrane suggesting a physical explanation for the formation of nuclear membrane invaginations.
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Affiliation(s)
- Régine Dazzoni
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248, CNRS, Université Bordeaux, INP-Bordeaux, F-33600, Pessac, France.,Cell Biophysics Laboratory, Ikerbasque Basque Foundation for Science, Instituto Biofísika (CSIC, UPV/EHU) and Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Axelle Grélard
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248, CNRS, Université Bordeaux, INP-Bordeaux, F-33600, Pessac, France
| | - Estelle Morvan
- Institut Européen de Chimie et Biologie, UMS3033, CNRS, Université Bordeaux, INSERM (US001), 2 rue Escarpit, Pessac, 33600, France
| | - Anthony Bouter
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248, CNRS, Université Bordeaux, INP-Bordeaux, F-33600, Pessac, France
| | - Christopher J Applebee
- Cell Biophysics Laboratory, Ikerbasque Basque Foundation for Science, Instituto Biofísika (CSIC, UPV/EHU) and Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Leioa, Spain.,Cell Biophysics Laboratory, Centre for Therapeutic Innovation & Department of Pharmacy and Pharmacology, & Department of Physics, University of Bath, Bath, United Kingdom
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248, CNRS, Université Bordeaux, INP-Bordeaux, F-33600, Pessac, France
| | - Banafshé Larijani
- Cell Biophysics Laboratory, Ikerbasque Basque Foundation for Science, Instituto Biofísika (CSIC, UPV/EHU) and Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Leioa, Spain. .,Cell Biophysics Laboratory, Centre for Therapeutic Innovation & Department of Pharmacy and Pharmacology, & Department of Physics, University of Bath, Bath, United Kingdom.
| | - Erick J Dufourc
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248, CNRS, Université Bordeaux, INP-Bordeaux, F-33600, Pessac, France.
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26
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Kasari V, Pochopien AA, Margus T, Murina V, Turnbull K, Zhou Y, Nissan T, Graf M, Nováček J, Atkinson GC, Johansson MJO, Wilson DN, Hauryliuk V. A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination/recycling. Nucleic Acids Res 2019; 47:8807-8820. [PMID: 31299085 PMCID: PMC7145556 DOI: 10.1093/nar/gkz600] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/14/2019] [Accepted: 07/11/2019] [Indexed: 11/12/2022] Open
Abstract
Translation is controlled by numerous accessory proteins and translation factors. In the yeast Saccharomyces cerevisiae, translation elongation requires an essential elongation factor, the ABCF ATPase eEF3. A closely related protein, New1, is encoded by a non-essential gene with cold sensitivity and ribosome assembly defect knock-out phenotypes. Since the exact molecular function of New1 is unknown, it is unclear if the ribosome assembly defect is direct, i.e. New1 is a bona fide assembly factor, or indirect, for instance due to a defect in protein synthesis. To investigate this, we employed yeast genetics, cryo-electron microscopy (cryo-EM) and ribosome profiling (Ribo-Seq) to interrogate the molecular function of New1. Overexpression of New1 rescues the inviability of a yeast strain lacking the otherwise strictly essential translation factor eEF3. The structure of the ATPase-deficient (EQ2) New1 mutant locked on the 80S ribosome reveals that New1 binds analogously to the ribosome as eEF3. Finally, Ribo-Seq analysis revealed that loss of New1 leads to ribosome queuing upstream of 3′-terminal lysine and arginine codons, including those genes encoding proteins of the cytoplasmic translational machinery. Our results suggest that New1 is a translation factor that fine-tunes the efficiency of translation termination or ribosome recycling.
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Affiliation(s)
- Villu Kasari
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 90187 Umeå, Sweden
| | - Agnieszka A Pochopien
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Tõnu Margus
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 90187 Umeå, Sweden
| | - Victoriia Murina
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 90187 Umeå, Sweden
| | - Kathryn Turnbull
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 90187 Umeå, Sweden
| | - Yang Zhou
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden
| | - Tracy Nissan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, 10691, Sweden.,School of Life Science, University of Sussex, Brighton, BN19RH, UK
| | - Michael Graf
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Jiří Nováček
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Gemma C Atkinson
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden
| | - Marcus J O Johansson
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 90187 Umeå, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
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27
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Adedipe F, Grubbs N, Coates B, Wiegmman B, Lorenzen M. Structural and functional insights into the Diabrotica virgifera virgifera ATP-binding cassette transporter gene family. BMC Genomics 2019; 20:899. [PMID: 31775611 PMCID: PMC6882327 DOI: 10.1186/s12864-019-6218-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The western corn rootworm, Diabrotica virgifera virgifera, is a pervasive pest of maize in North America and Europe, which has adapted to current pest management strategies. In advance of an assembled and annotated D. v. virgifera genome, we developed transcriptomic resources to use in identifying candidate genes likely to be involved in the evolution of resistance, starting with members of the ATP-binding cassette (ABC) transporter family. RESULTS In this study, 65 putative D. v. virgifera ABC (DvvABC) transporters were identified within a combined transcriptome assembly generated from embryonic, larval, adult male, and adult female RNA-sequence libraries. Phylogenetic analysis placed the deduced amino-acid sequences of the DvvABC transporters into eight subfamilies (A to H). To supplement our sequence data with functional analysis, we identified orthologs of Tribolium castaneum ABC genes which had previously been shown to exhibit overt RNA interference (RNAi) phenotypes. We identified eight such D. v. virgifera genes, and found that they were functionally similar to their T. castaneum counterparts. Interestingly, depletion of DvvABCB_39715 and DvvABCG_3712 transcripts in adult females produced detrimental reproductive and developmental phenotypes, demonstrating the potential of these genes as targets for RNAi-mediated insect control tactics. CONCLUSIONS By combining sequence data from four libraries covering three distinct life stages, we have produced a relatively comprehensive de novo transcriptome assembly for D. v. virgifera. Moreover, we have identified 65 members of the ABC transporter family and provided the first insights into the developmental and physiological roles of ABC transporters in this pest species.
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Affiliation(s)
- Folukemi Adedipe
- Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, 1566 Thomas Hall, Raleigh, NC, 27695-7613, USA
| | - Nathaniel Grubbs
- Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, 1566 Thomas Hall, Raleigh, NC, 27695-7613, USA
| | - Brad Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Brian Wiegmman
- Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, 1566 Thomas Hall, Raleigh, NC, 27695-7613, USA
| | - Marcé Lorenzen
- Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, 1566 Thomas Hall, Raleigh, NC, 27695-7613, USA.
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28
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Genome-wide identification of ABC transporters in monogeneans. Mol Biochem Parasitol 2019; 234:111234. [PMID: 31715209 DOI: 10.1016/j.molbiopara.2019.111234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/02/2019] [Accepted: 11/07/2019] [Indexed: 01/05/2023]
Abstract
ATP-Binding Cassette (ABC) transporters are proteins that actively mediate the transport of a wide variety of molecules, including drugs. Thus, in parasitology, ABC transporters have gained attention as potential targets for therapeutic drugs. Among the parasitic Platyhelminthes, ABC transporters have been identified and classified in a few species of Trematoda and Cestoda but not in Monogenea. Monogeneans are mainly ectoparasites of marine and freshwater fish, although they can also be found on other aquatic organisms. Severe epizootics caused by monogeneans have been reported around the world, mainly in confined and/or overcrowded fish. The purpose of this study was to identify the ABC transporters in four species of monogeneans (Gyrodactylus salaris, Protopolystoma xenopodis, Eudiplozoon nipponicum and Neobenedenia melleni) for which genomic resources are publicly available. For comparative purposes, ABC transporters were also identified in endoparasitic (Schistosoma mansoni and Echinococcus granulosus) and free-living (Macrostomun lignano and Schmidtea mediterranea) platyhelminths. Thirty-two putative ABC transporters were identified in the genome of G. salaris, 40 in the genome of P. xenopodis, 46 in the transcriptome of E. nipponicum and 9 in a rather limited ESTs set available for N. melleni. Of the eight ABC subfamilies (A-H) known in metazoans, subfamily H was the only one not found in any monogenean species. In contrast, ABCC was the best represented subfamily. Phylogenetic analyses showed a few cases of one-to-one orthologous relationships, which agree with results from other metazoan species. We found some monogenean ABC members related to subfamilies B, C and G involved in drug resistance in humans. This information may be useful for future functional studies on ABC transporters in monogeneans.
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29
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Identification of candidate ATP-binding cassette transporter gene family members in Diaphorina citri (Hemiptera: Psyllidae) via adult tissues transcriptome analysis. Sci Rep 2019; 9:15842. [PMID: 31676883 PMCID: PMC6825165 DOI: 10.1038/s41598-019-52402-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 10/15/2019] [Indexed: 12/12/2022] Open
Abstract
The ATP-binding cassette (ABC) transporters exist in all living organisms and play major roles in various biological functions by transporting a wide variety of substrates across membranes. The functions of ABC transporters in drug resistance have been extensively studied in vertebrates; however, they are rarely characterized in agricultural pests. The Asian citrus psyllid, Diaphorina citri, is one of the most damaging pests of the Citrus genus because of its transmission of Huanglongbing, also known as Yellow Dragon disease. In this study, the next-generation sequencing technique was applied to research the ABC transporters of D. citri. Fifty-three ABC transporter genes were found in the RNA-Seq data, and among these ABC transporters, 4, 4, 5, 2, 1, 4, 18 and 15 ABC proteins belonged to the ABCA-ABCH subfamilies, respectively. Different expression profiles of 52 genes between imidacloprid-resistant and imidacloprid-susceptible strains were studied by qRT-PCR; 5 ABCGs and 4 ABCHs were significantly upregulated in the imidacloprid-resistant strain. In addition, five of the nine upregulated genes were widely expressed in adult tissues in spatial expression analysis. The results suggest that these genes may play key roles in this phenotype. In general, this study contributed to our current understanding of D. citri resistance to insecticides.
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30
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Ousalem F, Singh S, Chesneau O, Hunt JF, Boël G. ABC-F proteins in mRNA translation and antibiotic resistance. Res Microbiol 2019; 170:435-447. [PMID: 31563533 DOI: 10.1016/j.resmic.2019.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/01/2019] [Accepted: 09/11/2019] [Indexed: 12/15/2022]
Abstract
The ATP binding cassette protein superfamily comprises ATPase enzymes which are, for the most part, involved in transmembrane transport. Within this superfamily however, some protein families have other functions unrelated to transport. One example is the ABC-F family, which comprises an extremely diverse set of cytoplasmic proteins. All of the proteins in the ABC-F family characterized to date act on the ribosome and are translation factors. Their common function is ATP-dependent modulation of the stereochemistry of the peptidyl transferase center (PTC) in the ribosome coupled to changes in its global conformation and P-site tRNA binding geometry. In this review, we give an overview of the function, structure, and theories for the mechanisms-of-action of microbial proteins in the ABC-F family, including those involved in mediating resistance to ribosome-binding antibiotics.
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Affiliation(s)
- Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Shikha Singh
- Department of Biological, 702A Sherman Fairchild Center, Columbia University, New York, NY, 10027, United States
| | - Olivier Chesneau
- Département de Microbiologie, Institut Pasteur, 75724, Paris Cedex 15, France.
| | - John F Hunt
- Department of Biological, 702A Sherman Fairchild Center, Columbia University, New York, NY, 10027, United States.
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005, Paris, France.
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New Thalidomide-Resembling Dicarboximides Target ABC50 Protein and Show Antileukemic and Immunomodulatory Activities. Biomolecules 2019; 9:biom9090446. [PMID: 31487824 PMCID: PMC6770581 DOI: 10.3390/biom9090446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 12/19/2022] Open
Abstract
We identified novel dicarboximides that were selectively cytotoxic towards human leukemia cells. Using chemical and biological methods, we characterized the biological activity, identified cellular protein targets and defined the mechanism of action of the test dicarboximides. The reported IC50 values (concentration required to reduce cell survival fraction to 50% of control) of selected dicarboximides were similar or lower than IC50 of registered anticancer drugs, for example cytarabine, sorafenib, irinotecan. Test compounds induced apoptosis in chronic myelogenous (K562) and acute lymphoblastic (MOLT-4) leukemia cells by activation of receptor and mitochondrial apoptotic pathways and increased the expression of proapoptotic genes (BAX, NOXA, HTRA2, TNFRSF10B, ESRRBL1). Selected dicarboximides displayed immunomodulatory activity and downregulated IKZF1 and IKZF3 transcription factors in K562 and MOLT-4 leukemia cells. ATP-binding cassette protein 50 (ABC50) was identified as a target for dicarboximides. Cancer cells with knocked down ABC50 showed increased resistance to dicarboximides. Based on the structure of dicarboximides and thalidomide, novel proteolysis-targeting chimeras (PROTACs) were synthesized and used as tools to downregulate ABC50 in leukemia cells.
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Genome-wide identification of ATP-binding cassette transporters and expression profiles in the Asian citrus psyllid, Diaphorina citri, exposed to imidacloprid. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 30:305-311. [DOI: 10.1016/j.cbd.2019.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 11/21/2022]
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Fung SW, Cheung PFY, Yip CW, Ng LWC, Cheung TT, Chong CCN, Lee C, Lai PBS, Chan AWH, Tsao GSW, Wong CH, Chan SL, Lo KW, Cheung ST. The ATP-binding cassette transporter ABCF1 is a hepatic oncofetal protein that promotes chemoresistance, EMT and cancer stemness in hepatocellular carcinoma. Cancer Lett 2019; 457:98-109. [PMID: 31100412 DOI: 10.1016/j.canlet.2019.05.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/10/2019] [Accepted: 05/08/2019] [Indexed: 02/07/2023]
Abstract
ATP-binding cassette (ABC) transporters mediate multidrug resistance and cancer stem cell properties in various model systems. Yet, their biological significance in cancers, especially in hepatocellular carcinoma (HCC), remains unclear. In this study, we investigated the function of ABCF1 in HCC and explored its potential as a therapeutic target. ABCF1 was highly expressed in fetal mouse livers but not in normal adult livers. ABCF1 expression was upregulated in HCCs. These results demonstrate that ABCF1 functions as a hepatic oncofetal protein. We further demonstrated elevated ABCF1 expression in HCC cells upon acquiring chemoresistance. Suppression of ABCF1 by siRNA sensitized both parental cells and chemoresistant cells to chemotherapeutic agents. Reversely, ABCF1 overexpression promoted chemoresistance and drug efflux. In addition, overexpression of ABCF1 enhanced migration, spheroid and colony formation and epithelial-mesenchymal transition (EMT) induction. RNA sequencing analysis revealed EMT inducers HIF1α/IL8 and Sox4 as potential mediators for the oncogenic effect of ABCF1 in HCC progression. Together, this study illustrates that ABCF1 is a novel potential therapeutic target for HCC treatment.
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Affiliation(s)
- Sze Wai Fung
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong; School of Biomedical Sciences, The University of Hong Kong, Hong Kong; Department of Surgery, The University of Hong Kong, Hong Kong
| | - Phyllis Fung-Yi Cheung
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong; Division of Solid Tumor Translational Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chi Wai Yip
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong; Department of Surgery, The University of Hong Kong, Hong Kong; RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Linda Wing-Chi Ng
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong
| | - Tan To Cheung
- Department of Surgery, The University of Hong Kong, Hong Kong
| | | | - Carol Lee
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong
| | - Paul Bo-San Lai
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong
| | - Anthony Wing-Hung Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong
| | | | - Chi-Hang Wong
- Department of Clinical Oncology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong
| | - Stephen Lam Chan
- Department of Clinical Oncology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong
| | - Kwok Wai Lo
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong
| | - Siu Tim Cheung
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong; Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong.
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He Q, Yan Z, Si F, Zhou Y, Fu W, Chen B. ATP-Binding Cassette (ABC) Transporter Genes Involved in Pyrethroid Resistance in the Malaria Vector Anopheles sinensis: Genome-Wide Identification, Characteristics, Phylogenetics, and Expression Profile. Int J Mol Sci 2019; 20:ijms20061409. [PMID: 30897799 PMCID: PMC6471920 DOI: 10.3390/ijms20061409] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/27/2022] Open
Abstract
background: The ATP-binding cassette (ABC) transporters family is one of the largest families of membrane proteins existing in all living organisms. Pyrethroid resistance has become the largest unique obstacle for mosquito control worldwide. ABC transporters are thought to be associated with pyrethroid resistance in some agricultural pests, but little information is known for mosquitoes. Herein, we investigated the diversity, location, characteristics, phylogenetics, and evolution of ABC transporter family of genes in the Anopheles sinensis genome, and identified the ABC transporter genes associated with pyrethroid resistance through expression profiles using RNA-seq and qPCR. Results: 61 ABC transporter genes are identified and divided into eight subfamilies (ABCA-H), located on 22 different scaffolds. Phylogenetic and evolution analyses with ABC transporters of A. gambiae, Drosophila melanogaster, and Homo sapiens suggest that the ABCD, ABCG, and ABCH subfamilies are monophyly, and that the ABCC and ABCG subfamilies have experienced a gene duplication event. Both RNA-seq and qPCR analyses show that the AsABCG28 gene is uniquely significantly upregulated gene in all three field pyrethroid-resistant populations (Anhui, Chongqing, and Yunnan provinces) in comparison with a laboratory-susceptible strain from Jiangsu province. The AsABCG28 is significantly upregulated at 12-h and 24-h after deltamethrin exposure in three-day-old female adults. Conclusion: This study provides the information frame for ABC transporter subfamily of genes, and lays an important basis for the better understanding and further research of ABC transporter function in insecticide toxification. The AsABCG28 gene is associated with pyrethroid detoxification, and it functions at later period in the detoxification process for xenobiotics transportation.
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Affiliation(s)
- Qiyi He
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China.
| | - Zhentian Yan
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China.
| | - Fengling Si
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China.
| | - Yong Zhou
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China.
| | - Wenbo Fu
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China.
| | - Bin Chen
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China.
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Murina V, Kasari M, Takada H, Hinnu M, Saha CK, Grimshaw JW, Seki T, Reith M, Putrinš M, Tenson T, Strahl H, Hauryliuk V, Atkinson GC. ABCF ATPases Involved in Protein Synthesis, Ribosome Assembly and Antibiotic Resistance: Structural and Functional Diversification across the Tree of Life. J Mol Biol 2018; 431:3568-3590. [PMID: 30597160 PMCID: PMC6723617 DOI: 10.1016/j.jmb.2018.12.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/11/2018] [Accepted: 12/15/2018] [Indexed: 10/27/2022]
Abstract
Within the larger ABC superfamily of ATPases, ABCF family members eEF3 in Saccharomyces cerevisiae and EttA in Escherichia coli have been found to function as ribosomal translation factors. Several other ABCFs including biochemically characterized VgaA, LsaA and MsrE confer resistance to antibiotics that target the peptidyl transferase center and exit tunnel of the ribosome. However, the diversity of ABCF subfamilies, the relationships among subfamilies and the evolution of antibiotic resistance (ARE) factors from other ABCFs have not been explored. To address this, we analyzed the presence of ABCFs and their domain architectures in 4505 genomes across the tree of life. We find 45 distinct subfamilies of ABCFs that are widespread across bacterial and eukaryotic phyla, suggesting that they were present in the last common ancestor of both. Surprisingly, currently known ARE ABCFs are not confined to a distinct lineage of the ABCF family tree, suggesting that ARE can readily evolve from other ABCF functions. Our data suggest that there are a number of previously unidentified ARE ABCFs in antibiotic producers and important human pathogens. We also find that ATPase-deficient mutants of all four E. coli ABCFs (EttA, YbiT, YheS and Uup) inhibit protein synthesis, indicative of their ribosomal function, and demonstrate a genetic interaction of ABCFs Uup and YheS with translational GTPase BipA involved in assembly of the 50S ribosome subunit. Finally, we show that the ribosome-binding resistance factor VmlR from Bacillus subtilis is localized to the cytoplasm, ruling out a role in antibiotic efflux.
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Affiliation(s)
- Victoriia Murina
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Marje Kasari
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Hiraku Takada
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Mariliis Hinnu
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Chayan Kumar Saha
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - James W Grimshaw
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Takahiro Seki
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 263-8522 Chiba, Japan
| | - Michael Reith
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Marta Putrinš
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden; University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
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Boucher MJ, Ghosh S, Zhang L, Lal A, Jang SW, Ju A, Zhang S, Wang X, Ralph SA, Zou J, Elias JE, Yeh E. Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites. PLoS Biol 2018; 16:e2005895. [PMID: 30212465 PMCID: PMC6155542 DOI: 10.1371/journal.pbio.2005895] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 09/25/2018] [Accepted: 08/28/2018] [Indexed: 12/20/2022] Open
Abstract
Malaria parasites (Plasmodium spp.) and related apicomplexan pathogens contain a nonphotosynthetic plastid called the apicoplast. Derived from an unusual secondary eukaryote-eukaryote endosymbiosis, the apicoplast is a fascinating organelle whose function and biogenesis rely on a complex amalgamation of bacterial and algal pathways. Because these pathways are distinct from the human host, the apicoplast is an excellent source of novel antimalarial targets. Despite its biomedical importance and evolutionary significance, the absence of a reliable apicoplast proteome has limited most studies to the handful of pathways identified by homology to bacteria or primary chloroplasts, precluding our ability to study the most novel apicoplast pathways. Here, we combine proximity biotinylation-based proteomics (BioID) and a new machine learning algorithm to generate a high-confidence apicoplast proteome consisting of 346 proteins. Critically, the high accuracy of this proteome significantly outperforms previous prediction-based methods and extends beyond other BioID studies of unique parasite compartments. Half of identified proteins have unknown function, and 77% are predicted to be important for normal blood-stage growth. We validate the apicoplast localization of a subset of novel proteins and show that an ATP-binding cassette protein ABCF1 is essential for blood-stage survival and plays a previously unknown role in apicoplast biogenesis. These findings indicate critical organellar functions for newly discovered apicoplast proteins. The apicoplast proteome will be an important resource for elucidating unique pathways derived from secondary endosymbiosis and prioritizing antimalarial drug targets.
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Affiliation(s)
- Michael J. Boucher
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sreejoyee Ghosh
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lichao Zhang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Avantika Lal
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Se Won Jang
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - An Ju
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Shuying Zhang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Xinzi Wang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Stuart A. Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic, Australia
| | - James Zou
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Joshua E. Elias
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ellen Yeh
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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Qu L, Jiang Y, Cheng C, Wu D, Meng B, Chen Z, Zhu Y, Shaw N, Ouyang S, Liu ZJ. Crystal Structure of ATP-Bound Human ABCF1 Demonstrates a Unique Conformation of ABC Proteins. Structure 2018; 26:1259-1265.e3. [PMID: 30017566 DOI: 10.1016/j.str.2018.05.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/28/2017] [Accepted: 05/29/2018] [Indexed: 01/21/2023]
Abstract
Gene translation requires the correct selection of start codon AUG in mRNA. ATP-binding cassette subfamily F member 1 (ABCF1) plays a key role in the accuracy of start codon selection. However, the function of human ABCF1 is not clearly understood. Here, we solve the crystal structure of an ATP-bound wild-type human ABCF1 at 2.3-Å resolution. The comparative studies indicate that the structure is in a pre-activation intermediate conformation. This conformation is stabilized by the interaction between ATP and protein. Thus, we propose that this conformation is an important step in the activation of ABCF1. This study extends our understanding of ABC (ATP-binding cassette) protein activation at the molecular level.
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Affiliation(s)
- Lu Qu
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, China; The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Yan Jiang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chongyun Cheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dong Wu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Bing Meng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenrong Chen
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Yanping Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Neil Shaw
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China.
| | - Zhi-Jie Liu
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, China; iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
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38
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Dukhovny A, Shlomai A, Sklan EH. The antiviral protein Viperin suppresses T7 promoter dependent RNA synthesis-possible implications for its antiviral activity. Sci Rep 2018; 8:8100. [PMID: 29802323 PMCID: PMC5970183 DOI: 10.1038/s41598-018-26516-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 05/11/2018] [Indexed: 12/28/2022] Open
Abstract
Viperin is a multifunctional interferon-inducible broad-spectrum antiviral protein. Viperin belongs to the S-Adenosylmethionine (SAM) superfamily of enzymes known to catalyze a wide variety of radical-mediated reactions. However, the exact mechanism by which viperin exerts its functions is still unclear. Interestingly, for many RNA viruses viperin was shown to inhibit viral RNA accumulation by interacting with different viral non-structural proteins. Here, we show that viperin inhibits RNA synthesis by bacteriophage T7 polymerase in mammalian cells. This inhibition is specific and occurs at the RNA level. Viperin expression significantly reduced T7-mediated cytoplasmic RNA levels. The data showing that viperin inhibits the bacteriophage T7 polymerase supports the conservation of viperin’s antiviral activity between species. These results highlight the possibility that viperin might utilize a broader mechanism of inhibition. Accordingly, our results suggest a novel mechanism involving polymerase inhibition and provides a tractable system for future mechanistic studies of viperin.
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Affiliation(s)
- Anna Dukhovny
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Amir Shlomai
- Department of Medicine D and the Liver Institute, Rabin Medical Center, Beilinson Hospital, Petach-Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella H Sklan
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
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39
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Mancarella C, Pasello M, Ventura S, Grilli A, Calzolari L, Toracchio L, Lollini PL, Donati DM, Picci P, Ferrari S, Scotlandi K. Insulin-Like Growth Factor 2 mRNA-Binding Protein 3 is a Novel Post-Transcriptional Regulator of Ewing Sarcoma Malignancy. Clin Cancer Res 2018; 24:3704-3716. [DOI: 10.1158/1078-0432.ccr-17-2602] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/12/2018] [Accepted: 04/23/2018] [Indexed: 11/16/2022]
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40
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Galatenko VV, Galatenko AV, Samatov TR, Turchinovich AA, Shkurnikov MY, Makarova JA, Tonevitsky AG. Comprehensive network of miRNA-induced intergenic interactions and a biological role of its core in cancer. Sci Rep 2018; 8:2418. [PMID: 29402894 PMCID: PMC5799291 DOI: 10.1038/s41598-018-20215-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/16/2018] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are a family of short noncoding RNAs that posttranscriptionally regulate gene expression and play an important role in multiple cellular processes. A significant percentage of miRNAs are intragenic, which is often functionally related to their host genes playing either antagonistic or synergistic roles. In this study, we constructed and analyzed the entire network of intergenic interactions induced by intragenic miRNAs. We further focused on the core of this network, which was defined as a union of nontrivial strongly connected components, i.e., sets of nodes (genes) mutually connected via directed paths. Both the entire network and its core possessed statistically significant non-random properties. Specifically, genes forming the core had high expression levels and low expression variance. Furthermore, the network core did not split into separate components corresponding to individual signalling or metabolic pathways, but integrated genes involved in key cellular processes, including DNA replication, transcription, protein homeostasis and cell metabolism. We suggest that the network core, consisting of genes mutually regulated by their intragenic miRNAs, could coordinate adjacent pathways or homeostatic control circuits, serving as a horizontal inter-circuit link. Notably, expression patterns of these genes had an efficient prognostic potential for breast and colorectal cancer patients.
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Affiliation(s)
- Vladimir V Galatenko
- Lomonosov Moscow State University, Leninskie Gory 1, 119991, Moscow, Russia. .,SRC Bioclinicum, Ugreshskaya str. 2/85, 115088, Moscow, Russia. .,Tauber Bioinformatics Research Center, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, 3498838, Haifa, Israel.
| | - Alexey V Galatenko
- Lomonosov Moscow State University, Leninskie Gory 1, 119991, Moscow, Russia
| | - Timur R Samatov
- SRC Bioclinicum, Ugreshskaya str. 2/85, 115088, Moscow, Russia.,Evotec International GmbH, Marie-Curie Str. 7, 37079, Göttingen, Germany
| | | | - Maxim Yu Shkurnikov
- P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, Second Botkinsky lane 3, 125284, Moscow, Russia
| | - Julia A Makarova
- P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, Second Botkinsky lane 3, 125284, Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova str. 32, 119991, Moscow, Russia
| | - Alexander G Tonevitsky
- SRC Bioclinicum, Ugreshskaya str. 2/85, 115088, Moscow, Russia. .,P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, Second Botkinsky lane 3, 125284, Moscow, Russia.
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Coots RA, Liu XM, Mao Y, Dong L, Zhou J, Wan J, Zhang X, Qian SB. m 6A Facilitates eIF4F-Independent mRNA Translation. Mol Cell 2017; 68:504-514.e7. [PMID: 29107534 DOI: 10.1016/j.molcel.2017.10.002] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 07/25/2017] [Accepted: 09/29/2017] [Indexed: 12/12/2022]
Abstract
In eukaryotic cells, protein synthesis typically begins with the binding of eIF4F to the 7-methylguanylate (m7G) cap found on the 5' end of the majority of mRNAs. Surprisingly, overall translational output remains robust under eIF4F inhibition. The broad spectrum of eIF4F-resistant translatomes is incompatible with cap-independent translation mediated by internal ribosome entry sites (IRESs). Here, we report that N6-methyladenosine (m6A) facilitates mRNA translation that is resistant to eIF4F inactivation. Depletion of the methyltransferase METTL3 selectively inhibits translation of mRNAs bearing 5' UTR methylation, but not mRNAs with 5' terminal oligopyrimidine (TOP) elements. We identify ABCF1 as a critical mediator of m6A-promoted translation under both stress and physiological conditions. Supporting the role of ABCF1 in m6A-facilitated mRNA translation, ABCF1-sensitive transcripts largely overlap with METTL3-dependent mRNA targets. By illustrating the scope and mechanism of eIF4F-independent mRNA translation, these findings reshape our current perceptions of cellular translational pathways.
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Affiliation(s)
- Ryan A Coots
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA; Graduate Field of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Xiao-Min Liu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Leiming Dong
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Jun Zhou
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Ji Wan
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Xingqian Zhang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA; Graduate Field of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
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42
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Guo H, Isserlin R, Emili A, Burniston JG. Exercise-responsive phosphoproteins in the heart. J Mol Cell Cardiol 2017; 111:61-68. [DOI: 10.1016/j.yjmcc.2017.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/14/2017] [Accepted: 08/01/2017] [Indexed: 01/14/2023]
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Sun H, Buchon N, Scott JG. Mdr65 decreases toxicity of multiple insecticides in Drosophila melanogaster. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 89:11-16. [PMID: 28803989 DOI: 10.1016/j.ibmb.2017.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/01/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
ABC transporters are ubiquitous membrane-bound proteins, present in both prokaryotes and eukaryotes. The major function of eukaryotic ABC transporters is to mediate the efflux of a variety of substrates (including xenobiotics) out of cells. ABC transporters have been widely investigated in humans, particularly for their involvement in multidrug resistance (MDR). Considerably less is known about their roles in transport and/or excretion in insects. ABC transporters are only known to function as exporters in insects. Drosophila melanogaster has 56 ABC transporter genes, including eight which are phylogenetically most similar to the human Mdr genes (ABCB1 clade). We investigated the role of ABC transporters in the ABCB1 clade in modulating the susceptibility to insecticides. We took advantage of the GAL4/UAS system in D. melanogaster to knockdown the expression levels of Mdr65, Mdr50, Mdr49 and ABCB6 using transgenic UAS-RNAi lines and conditional driver lines. The most notable effects were increased sensitivities to nine different insecticides by silencing of Mdr65. Furthermore, a null mutation of Mdr65 decreased the malathion, malaoxon and fipronil LC50 values by a factor of 1.9, 2.1 and 3.9, respectively. Altogether, this data demonstrates the critical role of ABC transporters, particularly Mdr65, in altering the toxicity of specific, structurally diverse, insecticides in D. melanogaster.
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Affiliation(s)
- Haina Sun
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA; Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Nicolas Buchon
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA
| | - Jeffrey G Scott
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA.
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Green VA, Pelkmans L. A Systems Survey of Progressive Host-Cell Reorganization during Rotavirus Infection. Cell Host Microbe 2017; 20:107-20. [PMID: 27414499 DOI: 10.1016/j.chom.2016.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/12/2016] [Accepted: 05/24/2016] [Indexed: 12/19/2022]
Abstract
Pathogen invasion is often accompanied by widespread alterations in cellular physiology, which reflects the hijacking of host factors and processes for pathogen entry and replication. Although genetic perturbation screens have revealed the complexity of host factors involved for numerous pathogens, it has remained challenging to temporally define the progression of events in host cell reorganization during infection. We combine high-confidence genome-scale RNAi screening of host factors required for rotavirus infection in human intestinal cells with an innovative approach to infer the trajectory of virus infection from fixed cell populations. This approach reveals a comprehensive network of host cellular processes involved in rotavirus infection and implicates AMPK in initiating the development of a rotavirus-permissive environment. Our work provides a powerful approach that can be generalized to order complex host cellular requirements along a trajectory of cellular reorganization during pathogen invasion.
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Affiliation(s)
- Victoria A Green
- Faculty of Sciences, Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
| | - Lucas Pelkmans
- Faculty of Sciences, Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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45
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Qasem-Abdullah H, Perach M, Livnat-Levanon N, Lewinson O. ATP binding and hydrolysis disrupt the high-affinity interaction between the heme ABC transporter HmuUV and its cognate substrate-binding protein. J Biol Chem 2017; 292:14617-14624. [PMID: 28710276 DOI: 10.1074/jbc.m117.779975] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Using the energy of ATP hydrolysis, ABC transporters catalyze the trans-membrane transport of molecules. In bacteria, these transporters partner with a high-affinity substrate-binding protein (SBP) to import essential micronutrients. ATP binding by Type I ABC transporters (importers of amino acids, sugars, peptides, and small ions) stabilizes the interaction between the transporter and the SBP, thus allowing transfer of the substrate from the latter to the former. In Type II ABC transporters (importers of trace elements, e.g. vitamin B12, heme, and iron-siderophores) the role of ATP remains debatable. Here we studied the interaction between the Yersinia pestis ABC heme importer (HmuUV) and its partner substrate-binding protein (HmuT). Using real-time surface plasmon resonance experiments and interaction studies in membrane vesicles, we find that in the absence of ATP the transporter and the SBP tightly bind. Substrate in excess inhibits this interaction, and ATP binding by the transporter completely abolishes it. To release the stable docked SBP from the transporter hydrolysis of ATP is required. Based on these results we propose a mechanism for heme acquisition by HmuUV-T where the substrate-loaded SBP docks to the nucleotide-free outward-facing conformation of the transporter. ATP binding leads to formation of an occluded state with the substrate trapped in the trans-membrane translocation cavity. Subsequent ATP hydrolysis leads to substrate delivery to the cytoplasm, release of the SBP, and resetting of the system. We propose that other Type II ABC transporters likely share the fundamentals of this mechanism.
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Affiliation(s)
- Hiba Qasem-Abdullah
- From the Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Michal Perach
- From the Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Nurit Livnat-Levanon
- From the Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa 31096, Israel
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46
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Sun H, Pu J, Chen F, Wang J, Han Z. Multiple ATP-binding cassette transporters are involved in insecticide resistance in the small brown planthopper, Laodelphax striatellus. INSECT MOLECULAR BIOLOGY 2017; 26:343-355. [PMID: 28299835 DOI: 10.1111/imb.12299] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
ATP-binding cassette (ABC) transporters are membrane-bound proteins involved in the movement of various substrates, including drugs and insecticides, across the lipid membrane. Demonstration of the role of human ABC transporters in multidrug resistance has led to speculation that they might be an important mechanism controlling the fate of insecticides in insects. However, the role of ABC transporters in insects remains largely unknown. The small brown planthopper, Laodelphax striatellus Fallén, has developed resistance to most of the insecticides used for its control. Our goals were to identify the ABC transporters in La. striatellus and to examine their involvement in resistance mechanisms, using related strains resistant to chlorpyrifos, deltamethrin and imidacloprid, compared with the susceptible strain. Based on the transcriptome of La. striatellus, 40 full-length ABC transporters belonging to the ABCA-ABCH subfamilies were identified. Quantitative PCR revealed that over 20% of genes were significantly up-regulated in different resistant strains, and eight genes from the ABCB/C/D/G subfamilies were up-regulated in all three resistant strains, compared with the susceptible strain. Furthermore, synergism studies showed verapamil significantly enhanced insecticide toxicity in various resistant strains but not in the susceptible strain. These results suggest that ABC transporters might be involved in resistance to multiple insecticides in La. striatellus.
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Affiliation(s)
- H Sun
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - J Pu
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - F Chen
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - J Wang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Z Han
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
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47
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Cerovska E, Elsnerova K, Vaclavikova R, Soucek P. The role of membrane transporters in ovarian cancer chemoresistance and prognosis. Expert Opin Drug Metab Toxicol 2017; 13:741-753. [PMID: 28511565 DOI: 10.1080/17425255.2017.1332179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Ovarian cancer has the highest mortality rate of all cancers in women. There is currently no effective method for early diagnosis, limiting the precision of clinical expectations. Predictions of therapeutic efficacy are currently not available either. Specifically, the development of chemoresistance against conventional chemotherapy poses a fundamental complication. Some membrane transporters have been reported to influence chemoresistance, which is often associated with a poor prognosis. Areas covered: The aim of this article is to review the existing information about membrane transporters and their role in both ovarian cancer chemoresistance and its outcomes. We then highlight limitations of current methodologies and suggest alternatives providing avenues for future research. Expert opinion: Membrane transporters play an important role in development of chemoresistance and affect prognosis of ovarian cancer patients; however, due to variations in methodology and in patient populations, their specific roles have yet to be clarified. For further evaluation of the clinical utility of membrane transporters, it is essential to validate results and improve methods for marker assessment across laboratories. A promising area for future research is to identify the genetic variability in potential markers in peripheral blood. These markers would then stratify patients into defined groups for optimal intervention.
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Affiliation(s)
- Ela Cerovska
- a Toxicogenomics Unit , National Institute of Public Health , Prague , Czech Republic
| | - Katerina Elsnerova
- a Toxicogenomics Unit , National Institute of Public Health , Prague , Czech Republic.,b 3rd Faculty of Medicine , Charles University , Prague , Czech Republic.,c Biomedical Center, Faculty of Medicine in Pilsen , Charles University , Pilsen , Czech Republic
| | - Radka Vaclavikova
- a Toxicogenomics Unit , National Institute of Public Health , Prague , Czech Republic.,c Biomedical Center, Faculty of Medicine in Pilsen , Charles University , Pilsen , Czech Republic
| | - Pavel Soucek
- a Toxicogenomics Unit , National Institute of Public Health , Prague , Czech Republic.,c Biomedical Center, Faculty of Medicine in Pilsen , Charles University , Pilsen , Czech Republic
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Wilcox SM, Arora H, Munro L, Xin J, Fenninger F, Johnson LA, Pfeifer CG, Choi KB, Hou J, Hoodless PA, Jefferies WA. The role of the innate immune response regulatory gene ABCF1 in mammalian embryogenesis and development. PLoS One 2017; 12:e0175918. [PMID: 28542262 PMCID: PMC5438103 DOI: 10.1371/journal.pone.0175918] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/03/2017] [Indexed: 12/15/2022] Open
Abstract
ABCF1 is an ABC transporter family protein that has been shown to regulate innate immune response and is a risk gene for autoimmune pancreatitis and arthritis. Unlike other members of ABC transporter family, ABCF1 lacks trans-membrane domains and is thought to function in translation initiation through an interaction with eukaryotic translation initiation factor 2 (eIF2). To study ABCF1 expression and function in development and disease, we used a single gene trap insertion in the Abcf1 gene in murine embryonic stem cells (ES cells) that allowed lineage tracing of the endogenous Abcf1 promoter by following the expression of a β-galactosidase reporter gene. From the ES cells, heterozygous mice (Abcf1+/-) were produced. No live born Abcf1-/- progeny were ever generated, and the lethality was not mouse strain-specific. Thus, we have determined that Abcf1 is an essential gene in development. Abcf1-/- mice were found to be embryonic lethal at 3.5 days post coitum (dpc), while Abcf1+/- mice appeared developmentally normal. Abcf1+/- mice were fertile and showed no significant differences in their anatomy when compared with their wild type littermates. The Abcf1 promoter was found to be active in all organs in adult mice, but varies in levels of expression in specific cell types within tissues. Furthermore, we observed high promoter activity in the blastocysts and embryos. Overall, Abcf1 expression in embryos is required for development and its expression in adults was highly correlated with actively proliferating and differentiating cell types.
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Affiliation(s)
- Sara M. Wilcox
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Hitesh Arora
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lonna Munro
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jian Xin
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Franz Fenninger
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Laura A. Johnson
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Cheryl G. Pfeifer
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kyung Bok Choi
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Juan Hou
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Pamela A. Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Developmental and Cell Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Wilfred A. Jefferies
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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49
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Tian L, Song T, He R, Zeng Y, Xie W, Wu Q, Wang S, Zhou X, Zhang Y. Genome-wide analysis of ATP-binding cassette (ABC) transporters in the sweetpotato whitefly, Bemisia tabaci. BMC Genomics 2017; 18:330. [PMID: 28446145 PMCID: PMC5405539 DOI: 10.1186/s12864-017-3706-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 04/12/2017] [Indexed: 12/12/2022] Open
Abstract
Background ABC transporter superfamily is one of the largest and ubiquitous groups of proteins. Because of their role in detoxification, insect ABC transporters have gained more attention in recent years. In this study, we annotated ABC transporters from a newly sequenced sweetpotato whitefly genome. Bemisia tabaci Q biotype is an emerging global invasive species that has caused extensive damages to field crops as well as ornamental plants. Results A total of 55 ABC transporters containing all eight described subfamilies (A to H) were identified in the B. tabaci Q genome, including 8 ABCAs, 3 ABCBs, 6 ABCCs, 2 ABCDs, 1 ABCE, 3 ABCFs, 23 ABCGs and 9 ABCHs. In comparison to other species, subfamilies G and H in both phloem- and blood-sucking arthropods are expanded. The temporal expression profiles of these 55 ABC transporters throughout B. tabaci developmental stages and their responses to imidacloprid, a neonicotinoid insecticide, were investigated using RNA-seq analysis. Furthermore, the mRNA expression of 24 ABC transporters (44% of the total) representing all eight subfamilies was confirmed by the quantitative real-time PCR (RT-qPCR). Furthermore, mRNA expression levels estimated by RT-qPCR and RNA-seq analyses were significantly correlated (r = 0.684, p < 0.01). Conclusions It is the first genome-wide analysis of the entire repertoire of ABC transporters in B. tabaci. The identification of these ABC transporters, their temporal expression profiles during B. tabaci development, and their response to a neonicotinoid insecticide lay the foundation for functional genomic understanding of their contribution to the invasiveness of B. tabaci. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3706-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lixia Tian
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tianxue Song
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Rongjun He
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Zeng
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wen Xie
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qingjun Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, 40546-0091, USA.
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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50
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Hopfner KP. Invited review: Architectures and mechanisms of ATP binding cassette proteins. Biopolymers 2017; 105:492-504. [PMID: 27037766 DOI: 10.1002/bip.22843] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/24/2016] [Accepted: 03/28/2016] [Indexed: 12/29/2022]
Abstract
ATP binding cassette (ABC) ATPases form chemo-mechanical engines and switches that function in a broad range of biological processes. Most prominently, a very large family of integral membrane NTPases-ABC transporters-catalyzes the import or export of a diverse molecules across membranes. ABC proteins are also important components of the chromosome segregation, recombination, and DNA repair machineries and regulate or catalyze critical steps of ribosomal protein synthesis. Recent structural and mechanistic studies draw interesting architectural and mechanistic parallels between diverse ABC proteins. Here, I review this state of our understanding how NTP-dependent conformational changes of ABC proteins drive diverse biological processes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 492-504, 2016.
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Affiliation(s)
- Karl-Peter Hopfner
- Department Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.,Center for Integrated Protein Science Munich, Ludwigs-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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