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Feijs-Žaja KLH, Ikenga NJ, Žaja R. Pathological and physiological roles of ADP-ribosylation: established functions and new insights. Biol Chem 2024:hsz-2024-0057. [PMID: 39066732 DOI: 10.1515/hsz-2024-0057] [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: 04/12/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
The posttranslational modification of proteins with poly(ADP-ribose) was discovered in the sixties. Since then, we have learned that the enzymes involved, the so-called poly(ADP-ribosyl)polymerases (PARPs), are transferases which use cofactor NAD+ to transfer ADP-ribose to their targets. Few PARPs are able to create poly(ADP-ribose), whereas the majority transfers a single ADP-ribose. In the last decade, hydrolases were discovered which reverse mono(ADP-ribosyl)ation, detection methods were developed and new substrates were defined, including nucleic acids. Despite the continued effort, relatively little is still known about the biological function of most PARPs. In this review, we summarise key functions of ADP-ribosylation and introduce emerging insights.
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Affiliation(s)
- Karla L H Feijs-Žaja
- 9165 Institute of Biochemistry and Molecular Biology, RWTH Aachen University , Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Nonso J Ikenga
- 9165 Institute of Biochemistry and Molecular Biology, RWTH Aachen University , Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Roko Žaja
- 9165 Institute of Biochemistry and Molecular Biology, RWTH Aachen University , Pauwelsstrasse 30, D-52074 Aachen, Germany
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2
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Mono-ADP-ribosylation by PARP10 inhibits Chikungunya virus nsP2 proteolytic activity and viral replication. Cell Mol Life Sci 2023; 80:72. [PMID: 36840772 PMCID: PMC9959937 DOI: 10.1007/s00018-023-04717-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/26/2023]
Abstract
Replication of viruses requires interaction with host cell factors and repression of innate immunity. Recent findings suggest that a subset of intracellular mono-ADP-ribosylating PARPs, which are induced by type I interferons, possess antiviral activity. Moreover, certain RNA viruses, including Chikungunya virus (CHIKV), encode mono-ADP-ribosylhydrolases. Together, this suggests a role for mono-ADP-ribosylation (MARylation) in host-virus conflicts, but the relevant substrates have not been identified. We addressed which PARP restricts CHIKV replication and identified PARP10 and PARP12. For PARP10, this restriction was dependent on catalytic activity. Replication requires processing of the non-structural polyprotein nsP1-4 by the protease located in nsP2 and the assembly of the four individual nsP1-nsP4 into a functional replication complex. PARP10 and PARP12 inhibited the production of nsP3, indicating a defect in polyprotein processing. The nsP3 protein encodes a macrodomain with de-MARylation activity, which is essential for replication. In support for MARylation affecting polyprotein processing, de-MARylation defective CHIKV replicons revealed reduced production of nsP2 and nsP3. We hypothesized that MARylation regulates the proteolytic function of nsP2. Indeed, we found that nsP2 is MARylated by PARP10 and, as a consequence, its proteolytic activity was inhibited. NsP3-dependent de-MARylation reactivated the protease. Hence, we propose that PARP10-mediated MARylation prevents polyprotein processing and consequently virus replication. Together, our findings provide a mechanistic explanation for the role of the viral MAR hydrolase in CHIKV replication.
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3
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Lüscher B, Verheirstraeten M, Krieg S, Korn P. Intracellular mono-ADP-ribosyltransferases at the host-virus interphase. Cell Mol Life Sci 2022; 79:288. [PMID: 35536484 PMCID: PMC9087173 DOI: 10.1007/s00018-022-04290-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 01/22/2023]
Abstract
The innate immune system, the primary defense mechanism of higher organisms against pathogens including viruses, senses pathogen-associated molecular patterns (PAMPs). In response to PAMPs, interferons (IFNs) are produced, allowing the host to react swiftly to viral infection. In turn the expression of IFN-stimulated genes (ISGs) is induced. Their products disseminate the antiviral response. Among the ISGs conserved in many species are those encoding mono-ADP-ribosyltransferases (mono-ARTs). This prompts the question whether, and if so how, mono-ADP-ribosylation affects viral propagation. Emerging evidence demonstrates that some mono-ADP-ribosyltransferases function as PAMP receptors and modify both host and viral proteins relevant for viral replication. Support for mono-ADP-ribosylation in virus–host interaction stems from the findings that some viruses encode mono-ADP-ribosylhydrolases, which antagonize cellular mono-ARTs. We summarize and discuss the evidence linking mono-ADP-ribosylation and the enzymes relevant to catalyze this reversible modification with the innate immune response as part of the arms race between host and viruses.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
| | - Maud Verheirstraeten
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
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4
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Li B, Wang Y, Pelz C, Moss J, Shemer R, Dor Y, Akkari YK, Canady PS, Naugler WE, Orloff S, Grompe M. In vitro expansion of cirrhosis derived liver epithelial cells with defined small molecules. Stem Cell Res 2021; 56:102523. [PMID: 34601385 DOI: 10.1016/j.scr.2021.102523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/30/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND & AIMS Mature hepatocytes have limited expansion capability in culture and rapidly loose key functions. Recently however, tissue culture conditions have been developed that permit rodent hepatocytes to proliferate and transform into progenitor-like cells with ductal characteristics in vitro. Analogous cells expressing both hepatic and duct markers can be found in human cirrhotic liver in vivo and may represent an expandable population. METHODS An in vitro culture system to expand epithelial cells from human end stage liver disease organs was developed by inhibiting the canonical TGF-β, Hedgehog and BMP pathways. RESULTS Human cirrhotic liver epithelial cells became highly proliferative in vitro. Both gene expression and DNA methylation site analyses revealed that cirrhosis derived epithelial liver cells were intermediate between normal hepatocytes and cholangiocytes. Mouse hepatocytes could be expanded under the same conditions and retained the ability to re-differentiate into hepatocytes upon transplantation. In contrast, human cirrhotic liver derived cells had only low re-differentiation capacity. CONCLUSIONS Epithelial cells of intermediate ductal-hepatocytic phenotype can be isolated from human cirrhotic livers and expanded in vitro. Unlike their murine counterparts they have limited liver repopulation potential.
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Affiliation(s)
- Bin Li
- Oregon Stem Cell Center, USA; Department of Pediatrics, Papé Family Institute, Oregon Health & Science University, Portland, OR, USA
| | - Yuhan Wang
- Oregon Stem Cell Center, USA; Department of Pediatrics, Papé Family Institute, Oregon Health & Science University, Portland, OR, USA
| | - Carl Pelz
- Oregon Stem Cell Center, USA; Department of Pediatrics, Papé Family Institute, Oregon Health & Science University, Portland, OR, USA
| | - Josh Moss
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Israel
| | - Yassmine K Akkari
- Cytogenetics Services and Molecular Pathology, Legacy Health, Portland, OR, USA
| | - Pamela S Canady
- Oregon Stem Cell Center, USA; Department of Pediatrics, Papé Family Institute, Oregon Health & Science University, Portland, OR, USA
| | - Willscott E Naugler
- Oregon Stem Cell Center, USA; School of Medicine, Division of Gastroenterology and Hepatology, Oregon Health & Science University, Portland, OR, USA
| | - Susan Orloff
- School of Medicine, Division of Gastroenterology and Hepatology, Oregon Health & Science University, Portland, OR, USA
| | - Markus Grompe
- Oregon Stem Cell Center, USA; Department of Pediatrics, Papé Family Institute, Oregon Health & Science University, Portland, OR, USA.
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5
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Tan A, Doig CL. NAD + Degrading Enzymes, Evidence for Roles During Infection. Front Mol Biosci 2021; 8:697359. [PMID: 34485381 PMCID: PMC8415550 DOI: 10.3389/fmolb.2021.697359] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
Declines in cellular nicotinamide adenine dinucleotide (NAD) contribute to metabolic dysfunction, increase susceptibility to disease, and occur as a result of pathogenic infection. The enzymatic cleavage of NAD+ transfers ADP-ribose (ADPr) to substrate proteins generating mono-ADP-ribose (MAR), poly-ADP-ribose (PAR) or O-acetyl-ADP-ribose (OAADPr). These important post-translational modifications have roles in both immune response activation and the advancement of infection. In particular, emergent data show viral infection stimulates activation of poly (ADP-ribose) polymerase (PARP) mediated NAD+ depletion and stimulates hydrolysis of existing ADP-ribosylation modifications. These studies are important for us to better understand the value of NAD+ maintenance upon the biology of infection. This review focuses specifically upon the NAD+ utilising enzymes, discusses existing knowledge surrounding their roles in infection, their NAD+ depletion capability and their influence within pathogenic infection.
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Affiliation(s)
- Arnold Tan
- Interdisciplinary Science and Technology Centre, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Craig L Doig
- Interdisciplinary Science and Technology Centre, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
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Al-Haj L, Khabar KSA. The intracellular pyrimidine 5'-nucleotidase NT5C3A is a negative epigenetic factor in interferon and cytokine signaling. Sci Signal 2018; 11:11/518/eaal2434. [PMID: 29463777 DOI: 10.1126/scisignal.aal2434] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The enzyme pyrimidine 5'-nucleotidase (NT5C3A), which mediates nucleotide catabolism, was previously thought to be restricted to blood cells. We showed that expression of the gene encoding NT5C3A was induced by type I interferons (IFNs) in multiple cell types and that NT5C3A suppressed cytokine production through inhibition of the nuclear factor κB (NF-κB) pathway. NT5C3A expression required both an intronic IFN-stimulated response element and the IFN-stimulated transcription factor IRF1. Overexpression of NT5C3A, but not of its catalytic mutants, suppressed IL-8 production by HEK293 cells. Whereas knockdown of NT5C3A enhanced tumor necrosis factor (TNF)-stimulated IL-8 production, it reduced the IFN-mediated suppression of Il8 expression. Overexpression of NT5C3A increased the abundance of NAD+ and the activation of the sirtuins SIRT1 and SIRT6, which are NAD+-dependent deacetylases. NT5C3A-stimulated sirtuin activity resulted in deacetylation of histone H3 and the NF-κB subunit RelA (also known as p65), both of which were associated with the proximal region of the Il8 promoter, thus repressing the transcription of Il8 Together, these data identify an anti-inflammatory pathway that depends on the catalytic activity of NT5C3A and functions as a negative feedback regulator of inflammatory cytokine signaling.
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Affiliation(s)
- Latifa Al-Haj
- King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Khalid S A Khabar
- King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia.
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7
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Lüscher B, Bütepage M, Eckei L, Krieg S, Verheugd P, Shilton BH. ADP-Ribosylation, a Multifaceted Posttranslational Modification Involved in the Control of Cell Physiology in Health and Disease. Chem Rev 2017; 118:1092-1136. [PMID: 29172462 DOI: 10.1021/acs.chemrev.7b00122] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Posttranslational modifications (PTMs) regulate protein functions and interactions. ADP-ribosylation is a PTM, in which ADP-ribosyltransferases use nicotinamide adenine dinucleotide (NAD+) to modify target proteins with ADP-ribose. This modification can occur as mono- or poly-ADP-ribosylation. The latter involves the synthesis of long ADP-ribose chains that have specific properties due to the nature of the polymer. ADP-Ribosylation is reversed by hydrolases that cleave the glycosidic bonds either between ADP-ribose units or between the protein proximal ADP-ribose and a given amino acid side chain. Here we discuss the properties of the different enzymes associated with ADP-ribosylation and the consequences of this PTM on substrates. Furthermore, the different domains that interpret either mono- or poly-ADP-ribosylation and the implications for cellular processes are described.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Laura Eckei
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Patricia Verheugd
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Brian H Shilton
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany.,Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario , Medical Sciences Building Room 332, London, Ontario Canada N6A 5C1
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8
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Monies D, Abou Al-Shaar H, Goljan EA, Al-Younes B, Al-Breacan MMA, Al-Saif MM, Wakil SM, Meyer BF, Khabar KSA, Bohlega S. Identification of a novel genetic locus underlying tremor and dystonia. Hum Genomics 2017; 11:25. [PMID: 29110692 PMCID: PMC5674688 DOI: 10.1186/s40246-017-0123-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 10/27/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Five affected individuals with syndromic tremulous dystonia, spasticity, and white matter disease from a consanguineous extended family covering a period of over 24 years are presented. A positional cloning approach utilizing genome-wide linkage, homozygozity mapping and whole exome sequencing was used for genetic characterization. The impact of a calmodulin-binding transcription activator 2, (CAMTA2) isoform 2, hypomorphic mutation on mRNA and protein abundance was studied using fluorescent reporter expression cassettes. Human brain sub-region cDNA libraries were used to study the expression pattern of CAMTA2 transcript variants. RESULTS Linkage analysis and homozygozity mapping localized the disease allele to a 2.1 Mb interval on chromosome 17 with a LOD score of 4.58. Whole exome sequencing identified a G>A change in the transcript variant 2 5'UTR of CAMTA2 that was only 6 bases upstream of the translation start site (c.-6G > A) (NM_001171166.1) and segregated with disease in an autosomal recessive manner. Transfection of wild type and mutant 5'UTR-linked fluorescent reporters showed no impact upon mRNA levels but a significant reduction in the protein fluorescent activity implying translation inhibition. CONCLUSIONS Mutation of CAMTA2 resulting in post-transcriptional inhibition of its own gene activity likely underlies a novel syndromic tremulous dystonia.
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Affiliation(s)
- Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital, and Research Centre, PO Box 3354, Riyadh, 11211, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
| | - Hussam Abou Al-Shaar
- Department of Neurosciences, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh, 11211, Saudi Arabia
| | - Ewa A Goljan
- Department of Genetics, King Faisal Specialist Hospital, and Research Centre, PO Box 3354, Riyadh, 11211, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Banan Al-Younes
- Department of Genetics, King Faisal Specialist Hospital, and Research Centre, PO Box 3354, Riyadh, 11211, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | | | - Maher Mohammed Al-Saif
- Biomolecular Medicine, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Salma M Wakil
- Department of Genetics, King Faisal Specialist Hospital, and Research Centre, PO Box 3354, Riyadh, 11211, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital, and Research Centre, PO Box 3354, Riyadh, 11211, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Biomolecular Medicine, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Saeed Bohlega
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia. .,Department of Neurosciences, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh, 11211, Saudi Arabia.
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9
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Li B, Dorrell C, Canaday PS, Pelz C, Haft A, Finegold M, Grompe M. Adult Mouse Liver Contains Two Distinct Populations of Cholangiocytes. Stem Cell Reports 2017; 9:478-489. [PMID: 28689996 PMCID: PMC5549808 DOI: 10.1016/j.stemcr.2017.06.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 06/01/2017] [Accepted: 06/01/2017] [Indexed: 02/07/2023] Open
Abstract
The biliary system plays an important role in several acquired and genetic disorders of the liver. We have previously shown that biliary duct epithelium contains cells giving rise to proliferative Lgr5+ organoids in vitro. However, it remained unknown whether all biliary cells or only a specific subset had this clonogenic activity. The cell surface protease ST14 was identified as a positive marker for the clonogenic subset of cholangiocytes and was used to separate clonogenic and non-clonogenic duct cells by fluorescence-activated cell sorting. Only ST14hi duct cells had the ability to generate organoids that could be serially passaged. The gene expression profiles of clonogenic and non-clonogenic duct cells were similar, but several hundred genes were differentially expressed. RNA fluorescence in situ hybridization showed that clonogenic duct cells are interspersed among regular biliary epithelium at a ∼1:3 ratio. We conclude that adult murine cholangiocytes can be subdivided into two populations differing in their proliferative capacity.
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Affiliation(s)
- Bin Li
- Oregon Stem Cell Center, Oregon Health and Science University, Portland, OR 97239, USA
| | - Craig Dorrell
- Oregon Stem Cell Center, Oregon Health and Science University, Portland, OR 97239, USA
| | - Pamela S Canaday
- Oregon Stem Cell Center, Oregon Health and Science University, Portland, OR 97239, USA
| | - Carl Pelz
- Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Annelise Haft
- Oregon Stem Cell Center, Oregon Health and Science University, Portland, OR 97239, USA
| | - Milton Finegold
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Markus Grompe
- Oregon Stem Cell Center, Oregon Health and Science University, Portland, OR 97239, USA; Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR 97239, USA; Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA.
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10
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Cabezas M, Mirkin CA, Mrksich M. Nanopatterned Extracellular Matrices Enable Cell-Based Assays with a Mass Spectrometric Readout. NANO LETTERS 2017; 17:1373-1377. [PMID: 28120616 PMCID: PMC5501326 DOI: 10.1021/acs.nanolett.6b04176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 01/24/2017] [Indexed: 05/27/2023]
Abstract
Cell-based assays are finding wider use in evaluating compounds in primary screens for drug development, yet it is still challenging to measure enzymatic activities as an end point in a cell-based assay. This paper reports a strategy that combines state-of-the-art cantilever free polymer pen lithography (PPL) with self-assembled monolayer laser desorption-ionization (SAMDI) mass spectrometry to guide cell localization and measure cellular enzymatic activities. Experiments are conducted with a 384 spot array, in which each spot is composed of ∼400 nanoarrays and each array has a 10 × 10 arrangement of 750 nm features that present extracellular matrix (ECM) proteins surrounded by an immobilized phosphopeptide. Cells attach to the individual nanoarrays, where they can be cultured and treated with small molecules, after which the media is removed and the cells are lysed. Phosphatase enzymes in the proximal lysate can then act on the immobilized phosphopeptide substrate to convert it to the dephosphorylated form. After the lysate is removed, the array is analyzed by SAMDI mass spectrometry to identify the extent of dephosphorylation and, therefore, the amount of enzyme activity in the cell. This novel approach of using nanopatterning to mediate cell adhesion and SAMDI to record enzyme activities in the proximal lysate will enable a broad range of cellular assays for applications in drug discovery and research not possible with conventional strategies.
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Affiliation(s)
- Maria
D. Cabezas
- Department of Chemistry and International Institute for Nanotechnology and Department of Biomedical
Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Chad A. Mirkin
- Department of Chemistry and International Institute for Nanotechnology and Department of Biomedical
Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department of Chemistry and International Institute for Nanotechnology and Department of Biomedical
Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department
of Cell and Molecular Biology, Feinberg
School of Medicine, 303
East Chicago Avenue, Chicago, Illinois 60611, United
States
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11
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Eckei L, Krieg S, Bütepage M, Lehmann A, Gross A, Lippok B, Grimm AR, Kümmerer BM, Rossetti G, Lüscher B, Verheugd P. The conserved macrodomains of the non-structural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases. Sci Rep 2017; 7:41746. [PMID: 28150709 PMCID: PMC5288732 DOI: 10.1038/srep41746] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/28/2016] [Indexed: 02/08/2023] Open
Abstract
Human pathogenic positive single strand RNA ((+)ssRNA) viruses, including Chikungunya virus, pose severe health problems as for many neither efficient vaccines nor therapeutic strategies exist. To interfere with propagation, viral enzymatic activities are considered potential targets. Here we addressed the function of the viral macrodomains, conserved folds of non-structural proteins of many (+)ssRNA viruses. Macrodomains are closely associated with ADP-ribose function and metabolism. ADP-ribosylation is a post-translational modification controlling various cellular processes, including DNA repair, transcription and stress response. We found that the viral macrodomains possess broad hydrolase activity towards mono-ADP-ribosylated substrates of the mono-ADP-ribosyltransferases ARTD7, ARTD8 and ARTD10 (aka PARP15, PARP14 and PARP10, respectively), reverting this post-translational modification both in vitro and in cells. In contrast, the viral macrodomains possess only weak activity towards poly-ADP-ribose chains synthesized by ARTD1 (aka PARP1). Unlike poly-ADP-ribosylglycohydrolase, which hydrolyzes poly-ADP-ribose chains to individual ADP-ribose units but cannot cleave the amino acid side chain - ADP-ribose bond, the different viral macrodomains release poly-ADP-ribose chains with distinct efficiency. Mutational and structural analyses identified key amino acids for hydrolase activity of the Chikungunya viral macrodomain. Moreover, ARTD8 and ARTD10 are induced by innate immune mechanisms, suggesting that the control of mono-ADP-ribosylation is part of a host-pathogen conflict.
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Affiliation(s)
- Laura Eckei
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany
| | - Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany
| | - Anne Lehmann
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany
| | - Annika Gross
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany
| | - Barbara Lippok
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany
| | - Alexander R Grimm
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Beate M Kümmerer
- Institute of Virology, University of Bonn Medical Centre, 53127 Bonn, Germany
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425, Jülich, Germany.,Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425, Jülich, Germany.,Department of Oncology, Hematology and Stem Cell Transplantation, Medical School, RWTH Aachen University, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany
| | - Patricia Verheugd
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany
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12
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Ede C, Chen X, Lin MY, Chen YY. Quantitative Analyses of Core Promoters Enable Precise Engineering of Regulated Gene Expression in Mammalian Cells. ACS Synth Biol 2016; 5:395-404. [PMID: 26883397 DOI: 10.1021/acssynbio.5b00266] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Inducible transcription systems play a crucial role in a wide array of synthetic biology circuits. However, the majority of inducible promoters are constructed from a limited set of tried-and-true promoter parts, which are susceptible to common shortcomings such as high basal expression levels (i.e., leakiness). To expand the toolbox for regulated mammalian gene expression and facilitate the construction of mammalian genetic circuits with precise functionality, we quantitatively characterized a panel of eight core promoters, including sequences with mammalian, viral, and synthetic origins. We demonstrate that this selection of core promoters can provide a wide range of basal gene expression levels and achieve a gradient of fold-inductions spanning 2 orders of magnitude. Furthermore, commonly used parts such as minimal CMV and minimal SV40 promoters were shown to achieve robust gene expression upon induction, but also suffer from high levels of leakiness. In contrast, a synthetic promoter, YB_TATA, was shown to combine low basal expression with high transcription rate in the induced state to achieve significantly higher fold-induction ratios compared to all other promoters tested. These behaviors remain consistent when the promoters are coupled to different genetic outputs and different response elements, as well as across different host-cell types and DNA copy numbers. We apply this quantitative understanding of core promoter properties to the successful engineering of human T cells that respond to antigen stimulation via chimeric antigen receptor signaling specifically under hypoxic environments. Results presented in this study can facilitate the design and calibration of future mammalian synthetic biology systems capable of precisely programmed functionality.
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Affiliation(s)
- Christopher Ede
- Department of Chemical and
Biomolecular Engineering, University of California—Los Angeles, Los Angeles, California 90095, United States
| | - Ximin Chen
- Department of Chemical and
Biomolecular Engineering, University of California—Los Angeles, Los Angeles, California 90095, United States
| | - Meng-Yin Lin
- Department of Chemical and
Biomolecular Engineering, University of California—Los Angeles, Los Angeles, California 90095, United States
| | - Yvonne Y. Chen
- Department of Chemical and
Biomolecular Engineering, University of California—Los Angeles, Los Angeles, California 90095, United States
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Human Cytokinome Analysis for Interferon Response. J Virol 2015; 89:7108-19. [PMID: 25926649 DOI: 10.1128/jvi.03729-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 04/21/2015] [Indexed: 01/06/2023] Open
Abstract
UNLABELLED Cytokines are a group of small secreted proteins that mediate a diverse range of immune and nonimmune responses to inflammatory and microbial stimuli. Only a few of these cytokines mount an antiviral response, including type I, II, and III interferons (IFNs). During viral infections and under inflammatory conditions, a number of cytokines and chemokines are coproduced with IFN; however, no systematic study exists on the interactions of the cytokine repertoire with the IFN response. Here, we performed the largest cytokine and chemokine screen (the human cytokinome, with >240 members) to investigate their modulation of type I and type II IFN responses in a cell line model. We evaluated the cytokine activities in both IFN-stimulated response element (ISRE) and IFN-γ activation sequence (GAS) reporter systems. Several cytokine clusters that augment either or both ISRE- and GAS-mediated responses to IFNs were derived from the screen. We identified novel modulators of IFN response-betacellulin (BTC), interleukin 11 (IL-11), and IL-17F-that caused time-dependent induction of the IFN response. The ability to induce endogenous IFN-β and IFN-stimulated genes varies among these cytokines and was largely dependent on Stat1, as assessed by Stat1 mutant fibroblasts. Certain cytokines appear to augment the IFN-β response through the NF-κB pathway. The novel IFN-like cytokines augmented the antiviral activity of IFN-α against several RNA viruses, including encephalomyocarditis virus, vesicular stomatitis virus, and influenza virus, in susceptible cell lines. Overall, the study represents a large-scale analysis of cytokines for enhancing the IFN response and identified cytokines capable of enhancing Stat1, IFN-induced gene expression, and antiviral activities. IMPORTANCE Innate immunity to viruses is an early defense system to ward off viruses. One mediator is interferon (IFN), which activates a cascade of biochemical events that aim to control the virus life cycle. In our work, we examined more than 200 cytokines, soluble mediators produced within the body as a result of infection, for the ability to enhance IFN action. We identified enhanced interactions with specific IFNs and cytokines. We also revealed that betacellulin, IL-17, and IL-11 cytokines have the novel property of enhancing the antiviral action of IFN against several viruses. These results demonstrate that the human genome codes for previously unknown proteins with unrelated functions that can augment the innate immunity to viruses. Knowing these interactions not only helps our understanding of immunity to viruses and emerging diseases, but can also lead to devising possible new therapeutics by enhancing the mediator of antiviral action itself, IFN.
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14
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Smurthwaite CA, Williams W, Fetsko A, Abbadessa D, Stolp ZD, Reed CW, Dharmawan A, Wolkowicz R. Genetic barcoding with fluorescent proteins for multiplexed applications. J Vis Exp 2015:52452. [PMID: 25938804 PMCID: PMC4541556 DOI: 10.3791/52452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Fluorescent proteins, fluorescent dyes and fluorophores in general have revolutionized the field of molecular cell biology. In particular, the discovery of fluorescent proteins and their genes have enabled the engineering of protein fusions for localization, the analysis of transcriptional activation and translation of proteins of interest, or the general tracking of individual cells and cell populations. The use of fluorescent protein genes in combination with retroviral technology has further allowed the expression of these proteins in mammalian cells in a stable and reliable manner. Shown here is how one can utilize these genes to give cells within a population of cells their own biosignature. As the biosignature is achieved with retroviral technology, cells are barcoded 'indefinitely'. As such, they can be individually tracked within a mixture of barcoded cells and utilized in more complex biological applications. The tracking of distinct populations in a mixture of cells is ideal for multiplexed applications such as discovery of drugs against a multitude of targets or the activation profile of different promoters. The protocol describes how to elegantly develop and amplify barcoded mammalian cells with distinct genetic fluorescent markers, and how to use several markers at once or one marker at different intensities. Finally, the protocol describes how the cells can be further utilized in combination with cell-based assays to increase the power of analysis through multiplexing.
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15
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Function and Regulation of the Mono-ADP-Ribosyltransferase ARTD10. Curr Top Microbiol Immunol 2014; 384:167-88. [DOI: 10.1007/82_2014_379] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Regulation of NF-κB signalling by the mono-ADP-ribosyltransferase ARTD10. Nat Commun 2013; 4:1683. [PMID: 23575687 DOI: 10.1038/ncomms2672] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 02/27/2013] [Indexed: 12/22/2022] Open
Abstract
Adenosine diphosphate-ribosylation is a post-translational modification mediated by intracellular and membrane-associated extracellular enzymes and many bacterial toxins. The intracellular enzymes modify their substrates either by poly-ADP-ribosylation, exemplified by ARTD1/PARP1, or by mono-ADP-ribosylation. The latter has been discovered only recently, and little is known about its physiological relevance. The founding member of mono-ADP-ribosyltransferases is ARTD10/PARP10. It possesses two ubiquitin-interaction motifs, a unique feature among ARTD/PARP enzymes. Here, we find that the ARTD10 ubiquitin-interaction motifs bind to K63-linked poly-ubiquitin, a modification that is essential for NF-κB signalling. We therefore studied the role of ARTD10 in this pathway. ARTD10 inhibits the activation of NF-κB and downstream target genes in response to interleukin-1β and tumour necrosis factor-α, dependent on catalytic activity and poly-ubiquitin binding of ARTD10. Mechanistically ARTD10 interferes with poly-ubiquitination of NEMO, which interacts with and is a substrate of ARTD10. Our findings identify a novel regulator of NF-κB signalling and provide evidence for cross-talk between K63-linked poly-ubiquitination and mono-ADP-ribosylation.
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Lienert F, Torella JP, Chen JH, Norsworthy M, Richardson RR, Silver PA. Two- and three-input TALE-based AND logic computation in embryonic stem cells. Nucleic Acids Res 2013; 41:9967-75. [PMID: 23982518 PMCID: PMC3834826 DOI: 10.1093/nar/gkt758] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Biological computing circuits can enhance our ability to control cellular functions and have potential applications in tissue engineering and medical treatments. Transcriptional activator-like effectors (TALEs) represent attractive components of synthetic gene regulatory circuits, as they can be designed de novo to target a given DNA sequence. We here demonstrate that TALEs can perform Boolean logic computation in mammalian cells. Using a split-intein protein-splicing strategy, we show that a functional TALE can be reconstituted from two inactive parts, thus generating two-input AND logic computation. We further demonstrate three-piece intein splicing in mammalian cells and use it to perform three-input AND computation. Using methods for random as well as targeted insertion of these relatively large genetic circuits, we show that TALE-based logic circuits are functional when integrated into the genome of mouse embryonic stem cells. Comparing construct variants in the same genomic context, we modulated the strength of the TALE-responsive promoter to improve the output of these circuits. Our work establishes split TALEs as a tool for building logic computation with the potential of controlling expression of endogenous genes or transgenes in response to a combination of cellular signals.
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Affiliation(s)
- Florian Lienert
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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Forst AH, Karlberg T, Herzog N, Thorsell AG, Gross A, Feijs KLH, Verheugd P, Kursula P, Nijmeijer B, Kremmer E, Kleine H, Ladurner AG, Schüler H, Lüscher B. Recognition of mono-ADP-ribosylated ARTD10 substrates by ARTD8 macrodomains. Structure 2013; 21:462-75. [PMID: 23473667 DOI: 10.1016/j.str.2012.12.019] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 12/13/2012] [Accepted: 12/21/2012] [Indexed: 10/27/2022]
Abstract
ADP-ribosyltransferases (ARTs) catalyze the transfer of ADP-ribose from NAD(+) onto substrates. Some ARTs generate in an iterative process ADP-ribose polymers that serve as adaptors for distinct protein domains. Other ARTs, exemplified by ARTD10, function as mono-ADP-ribosyltransferases, but it has been unclear whether this modification occurs in cells and how it is read. We observed that ARTD10 colocalized with ARTD8 and defined its macrodomains 2 and 3 as readers of mono-ADP-ribosylation both in vitro and in cells. The crystal structures of these two ARTD8 macrodomains and isothermal titration calorimetry confirmed their interaction with ADP-ribose. These macrodomains recognized mono-ADP-ribosylated ARTD10, but not poly-ADP-ribosylated ARTD1. This distinguished them from the macrodomain of macroH2A1.1, which interacted with poly- but not mono-ADP-ribosylated substrates. Moreover, Ran, an ARTD10 substrate, was also read by ARTD8 macrodomains. This identifies readers of mono-ADP-ribosylated proteins, defines their structures, and demonstrates the presence of this modification in cells.
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Affiliation(s)
- Alexandra H Forst
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany
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Feijs KLH, Verheugd P, Lüscher B. Expanding functions of intracellular resident mono-ADP-ribosylation in cell physiology. FEBS J 2013; 280:3519-29. [PMID: 23639026 DOI: 10.1111/febs.12315] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/25/2013] [Accepted: 04/29/2013] [Indexed: 12/12/2022]
Abstract
Poly-ADP-ribosylation functions in diverse signaling pathways, such as Wnt signaling and DNA damage repair, where its role is relatively well characterized. Contrarily, mono-ADP-ribosylation by for example ARTD10/PARP10 is much less understood. Recent developments hint at the involvement of mono-ADP-ribosylation in transcriptional regulation, the unfolded protein response, DNA repair, insulin secretion and immunity. Additionally, macrodomain-containing hydrolases, MacroD1, MacroD2 and C6orf130/TARG1, have been identified that make mono-ADP-ribosylation reversible. Complicating further progress is the lack of tools such as mono-ADP-ribose-specific antibodies. The currently known functions of mono-ADP-ribosylation are summarized here, as well as the available tools such as mass spectrometry to study this modification in vitro and in cells.
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Affiliation(s)
- Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
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Ge J, Wood DK, Weingeist DM, Prasongtanakij S, Navasumrit P, Ruchirawat M, Engelward BP. Standard fluorescent imaging of live cells is highly genotoxic. Cytometry A 2013; 83:552-60. [PMID: 23650257 DOI: 10.1002/cyto.a.22291] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/01/2013] [Accepted: 03/09/2013] [Indexed: 12/19/2022]
Abstract
Fluorescence microscopy is commonly used for imaging live mammalian cells. Here, we describe studies aimed at revealing the potential genotoxic effects of standard fluorescence microscopy. To assess DNA damage, a high throughput platform for single cell gel electrophoresis is used (e.g., the CometChip). Light emitted by three standard filters was studied: (a) violet light [340-380 nm], used to excite DAPI and other blue fluorophores, (b) blue light [460-500 nm] commonly used to image green fluorescent protein (GFP) and Calcein AM, and (c) green light [528-553 nm], useful for imaging red fluorophores. Results show that exposure of samples to light during imaging is indeed genotoxic even when the selected wavelengths are outside the range known to induce significant damage levels. Shorter excitation wavelengths and longer irradiation times lead to higher levels of DNA damage. We have also measured DNA damage in cells expressing enhanced GFP or stained with Calcein AM, a widely used green fluorophore. Data show that Calcein AM leads to a synergistic increase in the levels of DNA damage and that even cells that are not being directly imaged sustain significant DNA damage from exposure to indirect light. The nature of light-induced DNA damage during imaging was assessed using the Fpg glycosylase, an enzyme that enables quantification of oxidative DNA damage. Oxidative damage was evident in cells exposed to violet light. Furthermore, the Fpg glycosylase revealed the presence of oxidative DNA damage in blue-light exposed cells for which DNA damage was not detected using standard analysis conditions. Taken together, the results of these studies call attention to the potential confounding effects of DNA damage induced by standard imaging conditions, and identify wavelength, exposure time, and fluorophore as parameters that can be modulated to reduce light-induced DNA damage.
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Affiliation(s)
- Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Feijs KL, Kleine H, Braczynski A, Forst AH, Herzog N, Verheugd P, Linzen U, Kremmer E, Lüscher B. ARTD10 substrate identification on protein microarrays: regulation of GSK3β by mono-ADP-ribosylation. Cell Commun Signal 2013; 11:5. [PMID: 23332125 PMCID: PMC3627616 DOI: 10.1186/1478-811x-11-5] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/20/2012] [Indexed: 12/24/2022] Open
Abstract
Background Although ADP-ribosylation has been described five decades ago, only recently a distinction has been made between eukaryotic intracellular poly- and mono-ADP-ribosylating enzymes. Poly-ADP-ribosylation by ARTD1 (formerly PARP1) is best known for its role in DNA damage repair. Other polymer forming enzymes are ARTD2 (formerly PARP2), ARTD3 (formerly PARP3) and ARTD5/6 (formerly Tankyrase 1/2), the latter being involved in Wnt signaling and regulation of 3BP2. Thus several different functions of poly-ADP-ribosylation have been well described whereas intracellular mono-ADP-ribosylation is currently largely undefined. It is for example not known which proteins function as substrate for the different mono-ARTDs. This is partially due to lack of suitable reagents to study mono-ADP-ribosylation, which limits the current understanding of this post-translational modification. Results We have optimized a novel screening method employing protein microarrays, ProtoArrays®, applied here for the identification of substrates of ARTD10 (formerly PARP10) and ARTD8 (formerly PARP14). The results of this substrate screen were validated using in vitro ADP-ribosylation assays with recombinant proteins. Further analysis of the novel ARTD10 substrate GSK3β revealed mono-ADP-ribosylation as a regulatory mechanism of kinase activity by non-competitive inhibition in vitro. Additionally, manipulation of the ARTD10 levels in cells accordingly influenced GSK3β activity. Together these data provide the first evidence for a role of endogenous mono-ADP-ribosylation in intracellular signaling. Conclusions Our findings indicate that substrates of ADP-ribosyltransferases can be identified using protein microarrays. The discovered substrates of ARTD10 and ARTD8 provide the first sets of proteins that are modified by mono-ADP-ribosyltransferases in vitro. By studying one of the ARTD10 substrates more closely, the kinase GSK3β, we identified mono-ADP-ribosylation as a negative regulator of kinase activity.
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Affiliation(s)
- Karla Lh Feijs
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
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