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František Potužník J, Nešuta O, Škríba A, Voleníková B, Mititelu MB, Mancini F, Serianni V, Fernandez H, Spustová K, Trylčová J, Vopalensky P, Cahová H. Diadenosine Tetraphosphate (Ap 4 A) Serves as a 5' RNA Cap in Mammalian Cells. Angew Chem Int Ed Engl 2024; 63:e202314951. [PMID: 37934413 DOI: 10.1002/anie.202314951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/08/2023]
Abstract
The recent expansion of the field of RNA chemical modifications has changed our understanding of post-transcriptional gene regulation. Apart from internal nucleobase modifications, 7-methylguanosine was long thought to be the only eukaryotic RNA cap. However, the discovery of non-canonical RNA caps in eukaryotes revealed a new niche of previously undetected RNA chemical modifications. We are the first to report the existence of a new non-canonical RNA cap, diadenosine tetraphosphate (Ap4 A), in human and rat cell lines. Ap4 A is the most abundant dinucleoside polyphosphate in eukaryotic cells and can be incorporated into RNA by RNA polymerases as a non-canonical initiating nucleotide (NCIN). Using liquid chromatography-mass spectrometry (LC-MS), we show that the amount of capped Ap4 A-RNA is independent of the cellular concentration of Ap4 A. A decapping enzyme screen identifies two enzymes cleaving Ap4 A-RNA,NUDT2 and DXO, both of which also cleave other substrate RNAs in vitro. We further assess the translatability and immunogenicity of Ap4 A-RNA and show that although it is not translated, Ap4 A-RNA is recognized as self by the cell and does not elicit an immune response, making it a natural component of the transcriptome. Our findings open a previously unexplored area of eukaryotic RNA regulation.
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Affiliation(s)
- Jiří František Potužník
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Ondřej Nešuta
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Anton Škríba
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Barbora Voleníková
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Maria-Bianca Mititelu
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Flaminia Mancini
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Valentina Serianni
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Henri Fernandez
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Kristína Spustová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Jana Trylčová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Pavel Vopalensky
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Hana Cahová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
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2
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Yoon I, Kim U, Choi J, Kim S. Disease association and therapeutic routes of aminoacyl-tRNA synthetases. Trends Mol Med 2024; 30:89-105. [PMID: 37949787 DOI: 10.1016/j.molmed.2023.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are enzymes that catalyze the ligation of amino acids to tRNAs for translation. Beyond their traditional role in translation, ARSs have acquired regulatory functions in various biological processes (epi-translational functions). With their dual-edged activities, aberrant expression, secretion, and mutations of ARSs are associated with human diseases, including cancer, autoimmune diseases, and neurological diseases. The increasing numbers of newly unveiled activities and disease associations of ARSs have spurred interest in novel drug development, targeting disease-related catalytic and noncatalytic activities of ARSs as well as harnessing ARSs as sources for biological therapeutics. This review speculates how the translational and epi-translational activities of ARSs can be related and describes how their activities can be linked to diseases and drug discovery.
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Affiliation(s)
- Ina Yoon
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Uijoo Kim
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Jaeyoung Choi
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Sunghoon Kim
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea; College of Medicine, Gangnam Severance Hospital, Yonsei University, Seoul 06273, Republic of Korea; Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Incheon 21983, Republic of Korea.
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Tang Y, Behrens RT, St Gelais C, Wu S, Vivekanandan S, Razin E, Fang P, Wu L, Sherer N, Musier-Forsyth K. Human lysyl-tRNA synthetase phosphorylation promotes HIV-1 proviral DNA transcription. Nucleic Acids Res 2023; 51:12111-12123. [PMID: 37933844 PMCID: PMC10711549 DOI: 10.1093/nar/gkad941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 09/18/2023] [Accepted: 10/11/2023] [Indexed: 11/08/2023] Open
Abstract
Human lysyl-tRNA synthetase (LysRS) was previously shown to be re-localized from its normal cytoplasmic location in a multi-aminoacyl-tRNA synthetase complex (MSC) to the nucleus of HIV-1 infected cells. Nuclear localization depends on S207 phosphorylation but the nuclear function of pS207-LysRS in the HIV-1 lifecycle is unknown. Here, we show that HIV-1 replication was severely reduced in a S207A-LysRS knock-in cell line generated by CRISPR/Cas9; this effect was rescued by S207D-LysRS. LysRS phosphorylation up-regulated HIV-1 transcription, as did direct transfection of Ap4A, an upstream transcription factor 2 (USF2) activator that is synthesized by pS207-LysRS. Overexpressing an MSC-derived peptide known to stabilize LysRS MSC binding inhibited HIV-1 replication. Transcription of HIV-1 proviral DNA and other USF2 target genes was reduced in peptide-expressing cells. We propose that nuclear pS207-LysRS generates Ap4A, leading to activation of HIV-1 transcription. Our results suggest a new role for nuclear LysRS in facilitating HIV-1 replication and new avenues for antiviral therapy.
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Affiliation(s)
- Yingke Tang
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Center for RNA Biology, Ohio State University, Columbus, OH, USA
| | - Ryan T Behrens
- McArdle Laboratory for Cancer Research, Institute for Molecular Virology, & Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Corine St Gelais
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Center for RNA Biology, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Siqi Wu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, China
| | - Saravanan Vivekanandan
- Cellular and Molecular Mechanisms of Inflammation Program, National University of Singapore and The Hebrew University of Jerusalem (NUS–HUJ), Singapore
| | - Ehud Razin
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Israel
| | - Pengfei Fang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, China
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Nathan Sherer
- McArdle Laboratory for Cancer Research, Institute for Molecular Virology, & Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Center for RNA Biology, Ohio State University, Columbus, OH, USA
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Guo Y, Ollé L, Proaño-Pérez E, Aparicio C, Guerrero M, Muñoz-Cano R, Martín M. MRGPRX2 signaling involves the Lysyl-tRNA synthetase and MITF pathway. Front Immunol 2023; 14:1154108. [PMID: 37234172 PMCID: PMC10206166 DOI: 10.3389/fimmu.2023.1154108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/03/2023] [Indexed: 05/27/2023] Open
Abstract
MRGPRX2, a G-protein-coupled-seven transmembrane domain receptor, is mainly expressed in mast cells and neurons and is involved in skin immunity and pain. It is implicated in the pathophysiology of non-IgE-mediated immediate hypersensitivity and has been related to adverse drug reactions. Moreover, a role has been proposed in asthma, atopic dermatitis, contact dermatitis, and chronic spontaneous urticaria. Although it has a prominent role in disease, its signaling transduction is poorly understood. This study shows that MRGPRX2 activation with substance P increased Lysyl t-RNA synthetase (LysRS) translocation to the nucleus. LysRS is a moonlighting protein with a dual role in protein translation and IgE signaling in mast cells. Upon allergen- IgE-FcεRI crosslinking, LysRS is translocated to the nucleus and activates microphthalmia-associated transcription factor (MITF) activity. In this study, we found that MRGPRX2 triggering led to MITF phosphorylation and increased MITF activity. Therefore, overexpression of LysRS increased MITF activity after MRGPRX2 activation. MITF silencing reduced MRGPRX2-dependent calcium influx and mast cell degranulation. Furthermore, a MITF pathway inhibitor, ML329, impaired MITF expression, calcium influx, and mast cell degranulation. Moreover, drugs such as atracurium, vancomycin, and morphine, reported to induce MRGPRX2-dependent degranulation, increased MITF activity. Altogether, our data show that MRGPRX2 signaling enhances MITF activity, and its abrogation by silencing or inhibition resulted in defective MRGPRX2 degranulation. We conclude that MRGPRX2 signaling involves the LysRS and MITF pathway. Thus, MITF and MITF-dependent targets may be considered therapeutic approaches to treat pathologies where MRGPRX2 is implicated.
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Affiliation(s)
- Yanru Guo
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laia Ollé
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Elizabeth Proaño-Pérez
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Faculty of Health Sciences, Technical University of Ambato, Ambato, Ecuador
| | - Cristina Aparicio
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Mario Guerrero
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Rosa Muñoz-Cano
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Allergy Department, Hospital Clinic, University of Barcelona, Barcelona, Spain
- Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS), Instituto de Salud Carlos III, Madrid, Spain
| | - Margarita Martín
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS), Instituto de Salud Carlos III, Madrid, Spain
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Zegarra V, Mais CN, Freitag J, Bange G. The mysterious diadenosine tetraphosphate (AP4A). MICROLIFE 2023; 4:uqad016. [PMID: 37223742 PMCID: PMC10148737 DOI: 10.1093/femsml/uqad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/15/2023] [Accepted: 04/21/2023] [Indexed: 05/25/2023]
Abstract
Dinucleoside polyphosphates, a class of nucleotides found amongst all the Trees of Life, have been gathering a lot of attention in the past decades due to their putative role as cellular alarmones. In particular, diadenosine tetraphosphate (AP4A) has been widely studied in bacteria facing various environmental challenges and has been proposed to be important for ensuring cellular survivability through harsh conditions. Here, we discuss the current understanding of AP4A synthesis and degradation, protein targets, their molecular structure where possible, and insights into the molecular mechanisms of AP4A action and its physiological consequences. Lastly, we will briefly touch on what is known with regards to AP4A beyond the bacterial kingdom, given its increasing appearance in the eukaryotic world. Altogether, the notion that AP4A is a conserved second messenger in organisms ranging from bacteria to humans and is able to signal and modulate cellular stress regulation seems promising.
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Affiliation(s)
- Victor Zegarra
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Christopher-Nils Mais
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Johannes Freitag
- Department of Biology, Philipps University Marburg, Marburg 35043, Germany
| | - Gert Bange
- Corresponding author. Karl-von-Frisch Strasse 14, 35043 Marburg, Germany. E-mail:
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Frese M, Saumer P, Yuan Y, Herzog D, Höpfner D, Itzen A, Marx A. The Alarmone Diadenosine Tetraphosphate as a Cosubstrate for Protein AMPylation. Angew Chem Int Ed Engl 2023; 62:e202213279. [PMID: 36524454 PMCID: PMC10107192 DOI: 10.1002/anie.202213279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Diadenosine polyphosphates (Apn As) are non-canonical nucleotides whose cellular concentrations increase during stress and are therefore termed alarmones, signaling homeostatic imbalance. Their cellular role is poorly understood. In this work, we assessed Apn As for their usage as cosubstrates for protein AMPylation, a post-translational modification in which adenosine monophosphate (AMP) is transferred to proteins. In humans, AMPylation mediated by the AMPylator FICD with ATP as a cosubstrate is a response to ER stress. Herein, we demonstrate that Ap4 A is proficiently consumed for AMPylation by FICD. By chemical proteomics using a new chemical probe, we identified new potential AMPylation targets. Interestingly, we found that AMPylation targets of FICD may differ depending on the nucleotide cosubstrate. These results may suggest that signaling at elevated Ap4 A levels during cellular stress differs from when Ap4 A is present at low concentrations, allowing response to extracellular cues.
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Affiliation(s)
- Matthias Frese
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Philip Saumer
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Yizhi Yuan
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Doreen Herzog
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Dorothea Höpfner
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.,Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Aymelt Itzen
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.,Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
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MITF Downregulation Induces Death in Human Mast Cell Leukemia Cells and Impairs IgE-Dependent Degranulation. Int J Mol Sci 2023; 24:ijms24043515. [PMID: 36834926 PMCID: PMC9961600 DOI: 10.3390/ijms24043515] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Activating mutations in KIT (CD117) have been associated with several diseases, including gastrointestinal stromal tumors and mastocytosis. Rapidly progressing pathologies or drug resistance highlight the need for alternative treatment strategies. Previously, we reported that the adaptor molecule SH3 binding protein 2 (SH3BP2 or 3BP2) regulates KIT expression at the transcriptional level and microphthalmia-associated transcription factor (MITF) expression at the post-transcriptional level in human mast cells and gastrointestinal stromal tumor (GIST) cell lines. Lately, we have found that the SH3BP2 pathway regulates MITF through miR-1246 and miR-5100 in GIST. In this study, miR-1246 and miR-5100 were validated by qPCR in the SH3BP2-silenced human mast cell leukemia cell line (HMC-1). MiRNA overexpression reduces MITF and MITF-dependent target expression in HMC-1. The same pattern was observed after MITF silencing. In addition, MITF inhibitor ML329 treatment reduces MITF expression and affects the viability and cell cycle progression in HMC-1. We also examine whether MITF downregulation affected IgE-dependent mast cell degranulation. MiRNA overexpression, MITF silencing, and ML329 treatment reduced IgE-dependent degranulation in LAD2- and CD34+-derived mast cells. These findings suggest MITF may be a potential therapeutic target for allergic reactions and deregulated KIT mast-cell-mediated disorders.
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The Rosetta Stone Hypothesis-Based Interaction of the Tumor Suppressor Proteins Nit1 and Fhit. Cells 2023; 12:cells12030353. [PMID: 36766695 PMCID: PMC9913352 DOI: 10.3390/cells12030353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023] Open
Abstract
In previous studies, we have identified the tumor suppressor proteins Fhit (fragile histidine triad) and Nit1 (Nitrilase1) as interaction partners of β-catenin both acting as repressors of the canonical Wnt pathway. Interestingly, in D. melanogaster and C. elegans these proteins are expressed as NitFhit fusion proteins. According to the Rosetta Stone hypothesis, if proteins are expressed as fusion proteins in one organism and as single proteins in others, the latter should interact physically and show common signaling function. Here, we tested this hypothesis and provide the first biochemical evidence for a direct association between Nit1 and Fhit. In addition, size exclusion chromatography of purified recombinant human Nit1 showed a tetrameric structure as also previously observed for the NitFhit Rosetta Stone fusion protein Nft-1 in C. elegans. Finally, in line with the Rosetta Stone hypothesis we identified Hsp60 and Ubc9 as other common interaction partners of Nit1 and Fhit. The interaction of Nit1 and Fhit may affect their enzymatic activities as well as interaction with other binding partners.
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Zheng T, Jing M, Gong T, Yan J, Zeng J, Li Y. Deletion of the yqeK gene leads to the accumulation of Ap4A and reduced biofilm formation in Streptococcus mutans. Mol Oral Microbiol 2021; 37:9-21. [PMID: 34761536 DOI: 10.1111/omi.12356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/15/2021] [Accepted: 11/01/2021] [Indexed: 02/05/2023]
Abstract
Diadenosine-5',5'''-P1, P4-tetraphosphate (Ap4A) is a second messenger playing a crucial role in various life activities of bacteria. The increase of Ap4A expression is pleiotropic, resulting in an impairment in the formation of biofilm and other physiological functions in some bacteria. However, Ap4A function in Streptococcus mutans, an important pathogen related to dental caries, remains unknown. In this work, the Ap4A hydrolase, YqeK, was identified and characterized in S. mutans. Then, the effects of yqeK deletion on the growth, biofilm formation, and exopolysaccharide (EPS) quantification in S. mutans were determined by the assessment of the growth curve, crystal violet, and anthrone-sulfuric acid, respectively, and visualized by microscopy. The results showed that the in-frame deletion of the yqeK gene in S. mutans UA159 led to an increase in Ap4A levels, lag phase in the early growth, as well as decrease in biofilm formation and water-insoluble exopolysaccharide production. Global gene expression profile showed that the expression of 88 genes was changed in the yqeK mutant, and among these, 42 were upregulated and 46 were downregulated when compared with the wild-type S. mutans UA159. Upregulated genes were mainly involved in post-translational modification, protein turnover, and chaperones, while downregulated genes were mainly involved in carbohydrate transport and metabolism. Important virulence genes related to biofilms, such as gtfB, gtfC, and gbpC, were also significantly downregulated. In conclusion, these results indicated that YqeK affected the formation of biofilms and the expression of biofilm-related genes in S. mutans.
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Affiliation(s)
- Ting Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Meiling Jing
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jiangchuan Yan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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Dolot R, Krakowiak A, Kaczmarek R, Włodarczyk A, Pichlak M, Nawrot B. Biochemical, crystallographic and biophysical characterization of histidine triad nucleotide-binding protein 2 with different ligands including a non-hydrolyzable analog of Ap4A. Biochim Biophys Acta Gen Subj 2021; 1865:129968. [PMID: 34329705 DOI: 10.1016/j.bbagen.2021.129968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/02/2021] [Accepted: 07/25/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Human HINT2 is an important mitochondrial enzyme involved in many processes such as apoptosis and bioenergetics, but its endogenous substrates and the three-dimensional structure of the full-length protein have not been identified yet. METHODS An HPLC assay was used to test the hydrolytic activity of HINT2 against various adenosine, guanosine, and 2'-deoxyguanosine derivatives containing phosphate bonds of different types and different leaving groups. Data on binding affinity were obtained by microscale thermophoresis (MST). Crystal structures of HINT2, in its apo form and with a dGMP ligand, were resolved to atomic resolution. RESULTS HINT2 substrate specificity was similar to that of HINT1, but with the major exception of remarkable discrimination against substrates lacking the 2'-hydroxyl group. The biochemical results were consistent with binding affinity measurements. They showed a similar binding strength of AMP and GMP to HINT2, and much weaker binding of dGMP, in contrast to HINT1. A non-hydrolyzable analog of Ap4A (JB419) interacted with both proteins with similar Kd and Ap4A is the signaling molecule that can interact with hHINT1 and regulate the activity of some transcription factors. CONCLUSIONS Several forms of homo- and heterodimers of different lengths of N-terminally truncated polypeptides resulting from degradation of the full-length protein were described. Ser144 in HINT2 appeared to be functionally equivalent to Ser107 in HINT1 by supporting the protonation of the leaving group in the hydrolytic mechanism of HINT2. SIGNIFICANCE Our results should be considered in future studies on the natural function of HINT2 and its role in nucleotide prodrug processing.
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Affiliation(s)
- Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland.
| | - Agnieszka Krakowiak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland.
| | - Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Artur Włodarczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Marta Pichlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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The pLysRS-Ap 4A Pathway in Mast Cells Regulates the Switch from Host Defense to a Pathological State. Int J Mol Sci 2021; 22:ijms22115620. [PMID: 34070694 PMCID: PMC8198065 DOI: 10.3390/ijms22115620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/17/2022] Open
Abstract
The innate and adaptive immune systems play an essential role in host defense against pathogens. Various signal transduction pathways monitor and balance the immune system since an imbalance may promote pathological states such as allergy, inflammation, and cancer. Mast cells have a central role in the regulation of the innate/adaptive immune system and are involved in the pathogenesis of many inflammatory and allergic diseases by releasing inflammatory mediators such as histamines, proteases, chemotactic factors, and cytokines. Although various signaling pathways are associated with mast cell activation, our discovery and characterization of the pLysRS-Ap4A signaling pathway in these cells provided an additional important step towards a full understanding of the intracellular mechanisms involved in mast cell activation. In the present review, we will discuss in depth this signaling pathway’s contribution to host defense and the pathological state.
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12
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Guo Y, Proaño-Pérez E, Muñoz-Cano R, Martin M. Anaphylaxis: Focus on Transcription Factor Activity. Int J Mol Sci 2021; 22:ijms22094935. [PMID: 34066544 PMCID: PMC8124588 DOI: 10.3390/ijms22094935] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/22/2021] [Accepted: 05/02/2021] [Indexed: 12/11/2022] Open
Abstract
Anaphylaxis is a severe allergic reaction, rapid in onset, and can lead to fatal consequences if not promptly treated. The incidence of anaphylaxis has risen at an alarming rate in past decades and continues to rise. Therefore, there is a general interest in understanding the molecular mechanism that leads to an exacerbated response. The main effector cells are mast cells, commonly triggered by stimuli that involve the IgE-dependent or IgE-independent pathway. These signaling pathways converge in the release of proinflammatory mediators, such as histamine, tryptases, prostaglandins, etc., in minutes. The action and cell targets of these proinflammatory mediators are linked to the pathophysiologic consequences observed in this severe allergic reaction. While many molecules are involved in cellular regulation, the expression and regulation of transcription factors involved in the synthesis of proinflammatory mediators and secretory granule homeostasis are of special interest, due to their ability to control gene expression and change phenotype, and they may be key in the severity of the entire reaction. In this review, we will describe our current understanding of the pathophysiology of human anaphylaxis, focusing on the transcription factors' contributions to this systemic hypersensitivity reaction. Host mutation in transcription factor expression, or deregulation of their activity in an anaphylaxis context, will be updated. So far, the risk of anaphylaxis is unpredictable thus, increasing our knowledge of the molecular mechanism that leads and regulates mast cell activity will enable us to improve our understanding of how anaphylaxis can be prevented or treated.
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Affiliation(s)
- Yanru Guo
- Biochemistry Unit, Biomedicine Department, Faculty of Medicine, University of Barcelona, 08036 Barcelona, Spain; (Y.G.); (E.P.-P.)
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain;
| | - Elizabeth Proaño-Pérez
- Biochemistry Unit, Biomedicine Department, Faculty of Medicine, University of Barcelona, 08036 Barcelona, Spain; (Y.G.); (E.P.-P.)
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain;
| | - Rosa Muñoz-Cano
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain;
- Allergy Section, Pneumology Department, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain
- ARADyAL (Asthma, Drug Adverse Reactions and Allergy) Research Network, 28029 Madrid, Spain
| | - Margarita Martin
- Biochemistry Unit, Biomedicine Department, Faculty of Medicine, University of Barcelona, 08036 Barcelona, Spain; (Y.G.); (E.P.-P.)
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain;
- ARADyAL (Asthma, Drug Adverse Reactions and Allergy) Research Network, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-93-4024541; Fax: +34-93-4035882
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Zhang X, Liu B, Gao L, Yu H, Liu X, Du J, Xiao J, Liu Y, Gu L, Liao Q, Kang Z, Zhang Z, Zhang Y. Near-ideal van der Waals rectifiers based on all-two-dimensional Schottky junctions. Nat Commun 2021; 12:1522. [PMID: 33750797 PMCID: PMC7943806 DOI: 10.1038/s41467-021-21861-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
The applications of any two-dimensional (2D) semiconductor devices cannot bypass the control of metal-semiconductor interfaces, which can be severely affected by complex Fermi pinning effects and defect states. Here, we report a near-ideal rectifier in the all-2D Schottky junctions composed of the 2D metal 1 T'-MoTe2 and the semiconducting monolayer MoS2. We show that the van der Waals integration of the two 2D materials can efficiently address the severe Fermi pinning effect generated by conventional metals, leading to increased Schottky barrier height. Furthermore, by healing original atom-vacancies and reducing the intrinsic defect doping in MoS2, the Schottky barrier width can be effectively enlarged by 59%. The 1 T'-MoTe2/healed-MoS2 rectifier exhibits a near-unity ideality factor of ~1.6, a rectifying ratio of >5 × 105, and high external quantum efficiency exceeding 20%. Finally, we generalize the barrier optimization strategy to other Schottky junctions, defining an alternative solution to enhance the performance of 2D-material-based electronic devices.
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Affiliation(s)
- Xiankun Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Advanced Energy Materials and Technologies, University of Science and Technology Beijing, Beijing, People's Republic of China
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, People's Republic of China
| | - Baishan Liu
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Advanced Energy Materials and Technologies, University of Science and Technology Beijing, Beijing, People's Republic of China
| | - Li Gao
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Advanced Energy Materials and Technologies, University of Science and Technology Beijing, Beijing, People's Republic of China
| | - Huihui Yu
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Advanced Energy Materials and Technologies, University of Science and Technology Beijing, Beijing, People's Republic of China
| | - Xiaozhi Liu
- Collaborative Innovation Center of Quantum Matter, Beijing, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Junli Du
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Advanced Energy Materials and Technologies, University of Science and Technology Beijing, Beijing, People's Republic of China
| | - Jiankun Xiao
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Advanced Energy Materials and Technologies, University of Science and Technology Beijing, Beijing, People's Republic of China
| | - Yihe Liu
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Advanced Energy Materials and Technologies, University of Science and Technology Beijing, Beijing, People's Republic of China
| | - Lin Gu
- Collaborative Innovation Center of Quantum Matter, Beijing, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Qingliang Liao
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Advanced Energy Materials and Technologies, University of Science and Technology Beijing, Beijing, People's Republic of China
| | - Zhuo Kang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Advanced Energy Materials and Technologies, University of Science and Technology Beijing, Beijing, People's Republic of China
| | - Zheng Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Advanced Energy Materials and Technologies, University of Science and Technology Beijing, Beijing, People's Republic of China.
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, People's Republic of China.
| | - Yue Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Advanced Energy Materials and Technologies, University of Science and Technology Beijing, Beijing, People's Republic of China.
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, People's Republic of China.
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14
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Ferguson F, McLennan AG, Urbaniak MD, Jones NJ, Copeland NA. Re-evaluation of Diadenosine Tetraphosphate (Ap 4A) From a Stress Metabolite to Bona Fide Secondary Messenger. Front Mol Biosci 2020; 7:606807. [PMID: 33282915 PMCID: PMC7705103 DOI: 10.3389/fmolb.2020.606807] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/19/2020] [Indexed: 01/14/2023] Open
Abstract
Cellular homeostasis requires adaption to environmental stress. In response to various environmental and genotoxic stresses, all cells produce dinucleoside polyphosphates (NpnNs), the best studied of which is diadenosine tetraphosphate (Ap4A). Despite intensive investigation, the precise biological roles of these molecules have remained elusive. However, recent studies have elucidated distinct and specific signaling mechanisms for these nucleotides in prokaryotes and eukaryotes. This review summarizes these key discoveries and describes the mechanisms of Ap4A and Ap4N synthesis, the mediators of the cellular responses to increased intracellular levels of these molecules and the hydrolytic mechanisms required to maintain low levels in the absence of stress. The intracellular responses to dinucleotide accumulation are evaluated in the context of the "friend" and "foe" scenarios. The "friend (or alarmone) hypothesis" suggests that ApnN act as bona fide secondary messengers mediating responses to stress. In contrast, the "foe" hypothesis proposes that ApnN and other NpnN are produced by non-canonical enzymatic synthesis as a result of physiological and environmental stress in critically damaged cells but do not actively regulate mitigating signaling pathways. In addition, we will discuss potential target proteins, and critically assess new evidence supporting roles for ApnN in the regulation of gene expression, immune responses, DNA replication and DNA repair. The recent advances in the field have generated great interest as they have for the first time revealed some of the molecular mechanisms that mediate cellular responses to ApnN. Finally, areas for future research are discussed with possible but unproven roles for intracellular ApnN to encourage further research into the signaling networks that are regulated by these nucleotides.
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Affiliation(s)
- Freya Ferguson
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom.,Materials Science Institute, Lancaster University, Lancaster, United Kingdom
| | - Alexander G McLennan
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Michael D Urbaniak
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Nigel J Jones
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Nikki A Copeland
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom.,Materials Science Institute, Lancaster University, Lancaster, United Kingdom
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15
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Wang P, Xia H, Li Q, Wang F, Zhang L, Li T, Martyniuk P, Rogalski A, Hu W. Sensing Infrared Photons at Room Temperature: From Bulk Materials to Atomic Layers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1904396. [PMID: 31617328 DOI: 10.1002/smll.201904396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/08/2019] [Indexed: 05/06/2023]
Abstract
Room-temperature operating means a profound reduction of volume, power consumption, and cost for infrared (IR) photodetectors, which promise a wide range of applications in both military and civilian areas, including individual soldier equipment, automatic driving, etc. Inspired by this fact, since the beginning of 1990s, great efforts have been made in the development of uncooled thermal detectors. During the last two decades, similar efforts have been devoted using IR photon detectors, especially based on photovoltaic effects. Herein, the proven technologies, which have been commercialized with a large format, like InGaAs/InP pin diodes, InAsSb barrier detectors, and high-operating-temperature HgCdTe devices, are reviewed. The newly developed technology is emphasized, which has shown unique superiority in detecting mid-wavelength and long-wavelength IR signals, such as quantum cascade photodetectors. Finally, brand-new concept devices based on 2D materials are introduced, which are demonstrated to provide additional degrees of freedom in designing and fabricating room-temperature IR devices, for example, the construction of multi-heterojunctions without introducing lattice strain, the convenient integration of optical waveguides and electronic gratings. All information provided here aims to supply a full view of the progress and challenges of room-temperature IR detectors.
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Affiliation(s)
- Peng Wang
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yutian Road, Shanghai, 200083, China
- University of Chinese Academy of Science, No.19A Yuquan Road, Beijing, 100049, China
| | - Hui Xia
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yutian Road, Shanghai, 200083, China
- University of Chinese Academy of Science, No.19A Yuquan Road, Beijing, 100049, China
| | - Qing Li
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yutian Road, Shanghai, 200083, China
- University of Chinese Academy of Science, No.19A Yuquan Road, Beijing, 100049, China
| | - Fang Wang
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yutian Road, Shanghai, 200083, China
- University of Chinese Academy of Science, No.19A Yuquan Road, Beijing, 100049, China
| | - Lili Zhang
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yutian Road, Shanghai, 200083, China
- University of Chinese Academy of Science, No.19A Yuquan Road, Beijing, 100049, China
| | - Tianxin Li
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yutian Road, Shanghai, 200083, China
- University of Chinese Academy of Science, No.19A Yuquan Road, Beijing, 100049, China
| | - Piotr Martyniuk
- Institute of Applied Physics, Military University of Technology, 2 Kaliskiego Street, Warsaw, 00-908, Poland
| | - Antoni Rogalski
- Institute of Applied Physics, Military University of Technology, 2 Kaliskiego Street, Warsaw, 00-908, Poland
| | - Weida Hu
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yutian Road, Shanghai, 200083, China
- University of Chinese Academy of Science, No.19A Yuquan Road, Beijing, 100049, China
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