ABSTRACT
Aging, a complex biological process, plays key roles the development of multiple disorders referred as aging-related diseases involving cardiovascular diseases, stroke, neurodegenerative diseases, cancers, lipid metabolism-related diseases. ADP-ribosylation is a reversible modification onto proteins and nucleic acids to alter their structures and/or functions. Growing evidence support the importance of ADP-ribosylation and ADP-ribosylation-associated enzymes in aging and age-related diseases. In this review, we summarized ADP-ribosylation-associated proteins including ADP-ribosyl transferases, the ADP-ribosyl hydrolyses and ADP-ribose binding domains. Furthermore, we outlined the latest knowledge about regulation of ADP-ribosylation in the pathogenesis and progression of main aging-related diseases, organism aging and cellular senescence, and we also speculated the underlying mechanisms to better disclose this novel molecular network. Moreover, we discussed current issues and provided an outlook for future research, aiming to revealing the unknown bio-properties of ADP-ribosylation, and establishing a novel therapeutic perspective in aging-related diseases and health aging via targeting ADP-ribosylation.
Subject(s)
ADP-Ribosylation , Aging , Humans , Aging/metabolism , Aging/physiology , ADP-Ribosylation/physiology , Animals , Cellular Senescence/physiology , Neurodegenerative Diseases/metabolismABSTRACT
ADP-ribosylation has primarily been known as post-translational modification of proteins. As signalling strategy conserved in all domains of life, it modulates substrate activity, localisation, stability or interactions, thereby regulating a variety of cellular processes and microbial pathogenicity. Yet over the last years, there is increasing evidence of non-canonical forms of ADP-ribosylation that are catalysed by certain members of the ADP-ribosyltransferase family and go beyond traditional protein ADP-ribosylation signalling. New macromolecular targets such as nucleic acids and new ADP-ribose derivatives have been established, notably extending the repertoire of ADP-ribosylation signalling. Based on the physiological relevance known so far, non-canonical ADP-ribosylation deserves its recognition next to the traditional protein ADP-ribosylation modification and which we therefore review in the following.
Subject(s)
ADP-Ribosylation/physiology , ADP Ribose Transferases/chemistry , ADP Ribose Transferases/classification , ADP Ribose Transferases/physiology , Adenosine Diphosphate/metabolism , Guanosine/metabolism , N-Glycosyl Hydrolases/physiology , Poly(ADP-ribose) Polymerases/metabolism , Regulatory Sequences, Ribonucleic Acid , Signal Transduction , Structure-Activity Relationship , Thymidine/metabolism , Ubiquitin/metabolismABSTRACT
The intracellular pathogen Legionella pneumophila delivers more than 330 effectors into host cells by its Dot/Icm secretion system. Those effectors direct the biogenesis of the Legionella-containing vacuole (LCV) that permits its intracellular survival and replication. It has long been documented that the LCV is associated with mitochondria and a number of Dot/Icm effectors have been shown to target to this organelle. Yet, the biochemical function and host cell target of most of these effectors remain unknown. Here, we found that the Dot/Icm substrate Ceg3 (Lpg0080) is a mono-ADP-ribosyltransferase that localizes to the mitochondria in host cells where it attacks ADP/ATP translocases by ADP-ribosylation, and blunts their ADP/ATP exchange activity. The modification occurs on the second arginine residue in the -RRRMMM- element, which is conserved among all known ADP/ATP carriers from different organisms. Our results reveal modulation of host energy metabolism as a virulence mechanism for L. pneumophila.
Subject(s)
Energy Metabolism/physiology , Legionella pneumophila/pathogenicity , Mitochondrial ADP, ATP Translocases/metabolism , Vacuoles/microbiology , ADP-Ribosylation/physiology , HEK293 Cells , HeLa Cells , Humans , Legionnaires' Disease/metabolism , Legionnaires' Disease/microbiology , Vacuoles/physiology , VirulenceABSTRACT
Adenosine diphosphate (ADP)-ribosylation is a posttranslational modification involved in key regulatory events catalyzed by ADP-ribosyltransferases (ARTs). Substrate identification and localization of the mono-ADP-ribosyltransferase PARP12 at the trans-Golgi network (TGN) hinted at the involvement of ARTs in intracellular traffic. We find that Golgin-97, a TGN protein required for the formation and transport of a specific class of basolateral cargoes (e.g., E-cadherin and vesicular stomatitis virus G protein [VSVG]), is a PARP12 substrate. PARP12 targets an acidic cluster in the Golgin-97 coiled-coil domain essential for function. Its mutation or PARP12 depletion, delays E-cadherin and VSVG export and leads to a defect in carrier fission, hence in transport, with consequent accumulation of cargoes in a trans-Golgi/Rab11-positive intermediate compartment. In contrast, PARP12 does not control the Golgin-245-dependent traffic of cargoes such as tumor necrosis factor alpha (TNFα). Thus, the transport of different basolateral proteins to the plasma membrane is differentially regulated by Golgin-97 mono-ADP-ribosylation by PARP12. This identifies a selective regulatory mechanism acting on the transport of Golgin-97- vs. Golgin-245-dependent cargoes. Of note, PARP12 enzymatic activity, and consequently Golgin-97 mono-ADP-ribosylation, depends on the activation of protein kinase D (PKD) at the TGN during traffic. PARP12 is directly phosphorylated by PKD, and this is essential to stimulate PARP12 catalytic activity. PARP12 is therefore a component of the PKD-driven regulatory cascade that selectively controls a major branch of the basolateral transport pathway. We propose that through this mechanism, PARP12 contributes to the maintenance of E-cadherin-mediated cell polarity and cell-cell junctions.
Subject(s)
ADP-Ribosylation/physiology , Autoantigens/metabolism , Cadherins/metabolism , Cell Membrane/metabolism , Golgi Apparatus/metabolism , Golgi Matrix Proteins/metabolism , Poly(ADP-ribose) Polymerases/metabolism , Protein Kinase C/metabolism , Antigens, CD , Catalysis , HeLa Cells , Humans , Protein Transport , Tumor Necrosis Factor-alpha , trans-Golgi Network/metabolismABSTRACT
Poly(ADP-ribose) polymerases, PARPs, transfer ADP-ribose onto target proteins from nicotinamide adenine dinucleotide (NAD+). Current mass spectrometric analytical methods require proteolysis of target proteins, limiting the study of dynamic ADP-ribosylation on contiguous proteins. Herein, we present a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) method that facilitates multisite analysis of ADP-ribosylation. We observe divergent ADP-ribosylation dynamics for the catalytic domains of PARPs 14 and 15, with PARP15 modifying more sites on itself (+3-4 ADP-ribose) than the closely related PARP14 protein (+1-2 ADP-ribose)âdespite similar numbers of potential modification sites. We identify, for the first time, a minimal peptide fragment (18 amino-acids) that is preferentially modified by PARP14. Finally, we demonstrate through mutagenesis and chemical treatment with hydroxylamine that PARPs 14/15 prefer acidic residues. Our results highlight the utility of MALDI-TOF in the analysis of PARP target modifications and in elucidating the biochemical mechanism governing PARP target selection.
Subject(s)
ADP-Ribosylation/physiology , Chromatography, Thin Layer , Poly(ADP-ribose) Polymerases/metabolism , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Poly(ADP-ribose) Polymerases/genetics , Protein DomainsABSTRACT
ADP ribosylation is a reversible posttranslational modification mediated by poly(ADP-ribose)transferases (e.g., PARP1) and (ADP-ribosyl)hydrolases (e.g., ARH3 and PARG), ensuring synthesis and removal of mono-ADP-ribose or poly-ADP-ribose chains on protein substrates. Dysregulation of ADP ribosylation signaling has been associated with several neurodegenerative diseases, including Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease. Recessive ADPRHL2/ARH3 mutations are described to cause a stress-induced epileptic ataxia syndrome with developmental delay and axonal neuropathy (CONDSIAS). Here, we present two families with a neuropathy predominant disorder and homozygous mutations in ADPRHL2 We characterized a novel C26F mutation, demonstrating protein instability and reduced protein function. Characterization of the recurrent V335G mutant demonstrated mild loss of expression with retained enzymatic activity. Although the V335G mutation retains its mitochondrial localization, it has altered cytosolic/nuclear localization. This minimally affects basal ADP ribosylation but results in elevated nuclear ADP ribosylation during stress, demonstrating the vital role of ADP ribosylation reversal by ARH3 in DNA damage control.
Subject(s)
ADP-Ribosylation/genetics , Glycoside Hydrolases/genetics , Neuralgia/genetics , ADP-Ribosylation/physiology , Adolescent , Adult , Alleles , DNA Damage/physiology , DNA Repair/genetics , Family , Female , Glycoside Hydrolases/metabolism , Humans , Male , Mutation/genetics , Pedigree , Poly (ADP-Ribose) Polymerase-1 , Poly Adenosine Diphosphate Ribose/metabolismABSTRACT
The poly-adenosine diphosphate (ADP)-ribose polymerases (PARPs) are responsible for ADP-ribosylation, a reversible post-translational modification involved in many cellular processes including DNA damage repair, chromatin remodeling, regulation of translation and cell death. In addition to these physiological functions, recent studies have highlighted the role of PARPs in host defenses against viruses, either by direct antiviral activity, targeting certain steps of virus replication cycle, or indirect antiviral activity, via modulation of the innate immune response. This review focuses on the antiviral activity of PARPs, as well as strategies developed by viruses to escape their action.
Subject(s)
ADP-Ribosylation/physiology , Host Microbial Interactions/immunology , Poly(ADP-ribose) Polymerases/genetics , Viruses/immunology , ADP-Ribosylation/genetics , Cell Death , Host Microbial Interactions/genetics , Humans , Immunity, Innate , Immunomodulation , Poly(ADP-ribose) Polymerases/immunology , Protein Processing, Post-Translational , Viruses/geneticsABSTRACT
Adenosine diphosphate (ADP)-ribosylation is a nicotinamide adenine dinucleotide (NAD+)-dependent post-translational modification that is found on proteins as well as on nucleic acids. While ARTD1/PARP1-mediated poly-ADP-ribosylation has extensively been studied in the past 60 years, comparably little is known about the physiological function of mono-ADP-ribosylation and the enzymes involved in its turnover. Promising technological advances have enabled the development of innovative tools to detect NAD+ and NAD+/NADH (H for hydrogen) ratios as well as ADP-ribosylation. These tools have significantly enhanced our current understanding of how intracellular NAD dynamics contribute to the regulation of ADP-ribosylation as well as to how mono-ADP-ribosylation integrates into various cellular processes. Here, we discuss the recent technological advances, as well as associated new biological findings and concepts.
Subject(s)
Adenosine Diphosphate Ribose/metabolism , NAD/metabolism , Poly(ADP-ribose) Polymerases/metabolism , Protein Processing, Post-Translational/physiology , ADP-Ribosylation/physiology , Humans , Poly (ADP-Ribose) Polymerase-1/metabolismABSTRACT
Protein ADP-ribosylation is a reversible post-translational modification that regulates important cellular functions. The identification of modified proteins has proven challenging and has mainly been achieved via enrichment methodologies. Random mutagenesis was used here to develop an engineered Af1521 ADP-ribose binding macro domain protein with 1000-fold increased affinity towards ADP-ribose. The crystal structure reveals that two point mutations K35E and Y145R form a salt bridge within the ADP-ribose binding domain. This forces the proximal ribose to rotate within the binding pocket and, as a consequence, improves engineered Af1521 ADPr-binding affinity. Its use in our proteomic ADP-ribosylome workflow increases the ADP-ribosylated protein identification rates and yields greater ADP-ribosylome coverage. Furthermore, generation of an engineered Af1521 Fc fusion protein confirms the improved detection of cellular ADP-ribosylation by immunoblot and immunofluorescence. Thus, this engineered isoform of Af1521 can also serve as a valuable tool for the analysis of cellular ADP-ribosylation under in vivo conditions.
Subject(s)
ADP-Ribosylation/physiology , Adenosine Diphosphate Ribose/metabolism , Protein Engineering/methods , Proteins/metabolism , Adenosine Diphosphate Ribose/chemistry , Adenosine Diphosphate Ribose/genetics , Binding Sites , Carrier Proteins/genetics , Carrier Proteins/isolation & purification , Carrier Proteins/metabolism , HEK293 Cells , HeLa Cells , Humans , Models, Molecular , Mutagenesis , Protein Conformation , Protein Domains , Protein Processing, Post-Translational , Proteins/chemistry , Proteins/isolation & purification , Proteomics/methodsABSTRACT
CRISPR-Cas systems are bacterial anti-viral systems, and phages use anti-CRISPR proteins (Acrs) to inactivate these systems. Here, we report a novel mechanism by which AcrIF11 inhibits the type I-F CRISPR system. Our structural and biochemical studies demonstrate that AcrIF11 functions as a novel mono-ADP-ribosyltransferase (mART) to modify N250 of the Cas8f subunit, a residue required for recognition of the protospacer-adjacent motif, within the crRNA-guided surveillance (Csy) complex from Pseudomonas aeruginosa. The AcrIF11-mediated ADP-ribosylation of the Csy complex results in complete loss of its double-stranded DNA (dsDNA) binding activity. Biochemical studies show that AcrIF11 requires, besides Cas8f, the Cas7.6f subunit for binding to and modifying the Csy complex. Our study not only reveals an unprecedented mechanism of type I CRISPR-Cas inhibition and the evolutionary arms race between phages and bacteria but also suggests an approach for designing highly potent regulatory tools in the future applications of type I CRISPR-Cas systems.
Subject(s)
CRISPR-Associated Proteins/antagonists & inhibitors , CRISPR-Cas Systems/physiology , Viral Proteins/metabolism , ADP-Ribosylation/physiology , Bacterial Proteins/genetics , Bacteriophages/genetics , CRISPR-Associated Proteins/genetics , CRISPR-Associated Proteins/metabolism , CRISPR-Cas Systems/genetics , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , Cryoelectron Microscopy/methods , DNA/metabolism , Models, Molecular , RNA, Bacterial/metabolism , Viral Proteins/geneticsABSTRACT
ADP-ribosylation (ADPr) is a post-translational modification that plays pivotal roles in a wide range of cellular processes. Mass spectrometry (MS)-based analysis of ADPr under physiological conditions, without relying on genetic or chemical perturbation, has been hindered by technical limitations. Here, we describe the applicability of activated ion electron transfer dissociation (AI-ETD) for MS-based proteomics analysis of physiological ADPr using our unbiased Af1521 enrichment strategy. To benchmark AI-ETD, we profile 9,000 ADPr peptides mapping to >5,000 unique ADPr sites from a limited number of cells exposed to oxidative stress and identify 120% and 28% more ADPr peptides compared to contemporary strategies using ETD and electron-transfer higher-energy collisional dissociation (EThcD), respectively. Under physiological conditions, AI-ETD identifies 450 ADPr sites on low-abundant proteins, including in vivo cysteine modifications on poly(ADP-ribosyl)polymerase (PARP) 8 and tyrosine modifications on PARP14, hinting at specialist enzymatic functions for these enzymes. Collectively, our data provide insights into the physiological regulation of ADPr.
Subject(s)
ADP-Ribosylation/physiology , Electrons , Adenosine Diphosphate Ribose/metabolism , HeLa Cells , Humans , Ions , Poly (ADP-Ribose) Polymerase-1/metabolismABSTRACT
Poly-(ADP)-ribose polymerases (PARPs) are a family of 17 enzymes in humans that have diverse roles in cell physiology including DNA damage repair, transcription, innate immunity, and regulation of signaling pathways. The modular domain architecture of PARPs gives rise to this functional diversity. PARPs catalyze the transfer of ADP-ribose from nicotinamide adenine dinucleotide (NAD+) to targets-proteins and poly-nucleic acids. This enigmatic post-translational modification comes in two varieties: the transfer of a single unit of ADP-ribose, known as mono-ADP-ribosylation (MARylation) or the transfer of multiple units of ADP-ribose, known as poly-ADP-ribosylation (PARylation). Emerging data shows that PARPs are regulated at multiple levels to control when and where PARP-mediated M/PARylation occurs in cells. In this review, we will discuss the latest knowledge regarding the regulation of PARPs in cells: from transcription and protein stability to subcellular localization and modulation of catalytic activity.
Subject(s)
Poly(ADP-ribose) Polymerases/metabolism , ADP-Ribosylation/genetics , ADP-Ribosylation/physiology , Animals , Humans , NAD/genetics , NAD/metabolism , Poly ADP Ribosylation/genetics , Poly ADP Ribosylation/physiology , Poly(ADP-ribose) Polymerases/geneticsABSTRACT
The posttranslational modifications (PTMs) ADP-ribosylation and phosphorylation are important regulators of cellular pathways, and while mass spectrometry (MS)-based methods for the study of protein phosphorylation are well developed, protein ADP-ribosylation methodologies are still in a rapidly developing stage. The method described in this chapter uses immobilized metal affinity chromatography (IMAC), a phosphoenrichment matrix, to enrich ADP-ribosylated peptides which have been cleaved down to their phosphoribose attachment sites by a phosphodiesterase, thus isolating the ADP-ribosylated and phosphorylated proteomes simultaneously. To achieve the robust, relative quantification of PTM-level changes we have incorporated dimethyl labeling, a straightforward and economical choice which can be used on lysate from any cell type, including primary tissue. The entire pipeline has been optimized to work in ADP-ribosylation-compatible buffers and with protease-laden lysate from macrophage cells.
Subject(s)
ADP-Ribosylation/physiology , Adenosine Diphosphate Ribose/metabolism , Macrophages/metabolism , Phosphorylation/physiology , Animals , Cell Line , Humans , Mice , Peptides/metabolism , Phosphoric Diester Hydrolases/metabolism , Protein Processing, Post-Translational/physiology , Proteome/metabolism , Proteomics/methods , RAW 264.7 Cells , Rabbits , Tandem Mass Spectrometry/methodsABSTRACT
As more cases of COVID-19 are studied and treated worldwide, it had become apparent that the lethal and most severe cases of pneumonia are due to an out-of-control inflammatory response to the SARS-CoV-2 virus. I explored the putative causes of this specific feature through a detailed genomic comparison with the closest SARS-CoV-2 relatives isolated from bats, as well as previous coronavirus strains responsible for the previous epidemics (SARS-CoV and MERS-CoV). The high variability region of the nsp3 protein was confirmed to exhibit the most variations between closest strains. It was then studied in the context of physiological and molecular data available in the literature. A number of convergent findings suggest de-mono-ADP-ribosylation (de-MARylation) of STAT1 by the SARS-CoV-2 nsp3 as a putative cause of the cytokine storm observed in the most severe cases of COVID-19. This may suggest new therapeutic approaches and help in designing assays to predict the virulence of naturally circulating SARS-like animal coronaviruses.
Subject(s)
ADP-Ribosylation/physiology , Betacoronavirus/genetics , Cytokine Release Syndrome/pathology , STAT1 Transcription Factor/metabolism , Viral Nonstructural Proteins/metabolism , Amino Acid Sequence/genetics , Angiotensin-Converting Enzyme 2 , COVID-19 , Coronavirus Infections/pathology , Coronavirus Papain-Like Proteases , Humans , Inflammation/pathology , Inflammation/virology , Middle East Respiratory Syndrome Coronavirus/genetics , Pandemics , Peptidyl-Dipeptidase A/biosynthesis , Peptidyl-Dipeptidase A/genetics , Pneumonia, Viral/pathology , Severe acute respiratory syndrome-related coronavirus/genetics , SARS-CoV-2 , Sequence Homology , Viral Nonstructural Proteins/geneticsABSTRACT
ADP-ribosylation is an intricate and versatile posttranslational modification involved in the regulation of a vast variety of cellular processes in all kingdoms of life. Its complexity derives from the varied range of different chemical linkages, including to several amino acid side chains as well as nucleic acids termini and bases, it can adopt. In this review, we provide an overview of the different families of (ADP-ribosyl)hydrolases. We discuss their molecular functions, physiological roles, and influence on human health and disease. Together, the accumulated data support the increasingly compelling view that (ADP-ribosyl)hydrolases are a vital element within ADP-ribosyl signaling pathways and they hold the potential for novel therapeutic approaches as well as a deeper understanding of ADP-ribosylation as a whole.
Subject(s)
ADP-Ribosylation/physiology , Adenosine Diphosphate/metabolism , Hydrolases/chemistry , Hydrolases/metabolism , Humans , Hydrolases/classification , Protein Domains , Structure-Activity RelationshipABSTRACT
ADP-ribosylation (ADPRylation) is a posttranslational modification of proteins discovered nearly six decades ago, but many important questions remain regarding its molecular functions and biological roles, as well as the activity of the ADP-ribose (ADPR) transferase enzymes (PARP family members) that catalyze it. Growing evidence indicates that PARP-mediated ADPRylation events are key regulators of the protein biosynthetic pathway, leading from rDNA transcription and ribosome biogenesis to mRNA synthesis, processing, and translation. In this review we describe the role of PARP proteins and ADPRylation in all facets of this pathway. PARP-1 and its enzymatic activity are key regulators of rDNA transcription, which is a critical step in ribosome biogenesis. An emerging role of PARPs in alternative splicing of mRNAs, as well as direct ADPRylation of mRNAs, highlight the role of PARP members in RNA processing. Furthermore, PARP activity, stimulated by cellular stresses, such as viral infections and ER stress, leads to the regulation of mRNA stability and protein synthesis through posttranscriptional mechanisms. Dysregulation of PARP activity in these processes can promote disease states. Collectively, these results highlight the importance of PARP family members and ADPRylation in gene regulation, mRNA processing, and protein abundance. Future studies in these areas will yield new insights into the fundamental mechanisms and a broader utility for PARP-targeted therapeutic agents.
Subject(s)
ADP-Ribosylation/physiology , Gene Expression/physiology , Poly(ADP-ribose) Polymerases/metabolism , Protein Biosynthesis/physiology , Proteostasis/physiology , Animals , Humans , Protein Processing, Post-Translational , RNA/metabolismABSTRACT
Poly-adenosine diphosphate-ribose polymerases (PARPs) promote ADP-ribosylation, a highly conserved, fundamental posttranslational modification (PTM). PARP catalytic domains transfer the ADP-ribose moiety from NAD+ to amino acid residues of target proteins, leading to mono- or poly-ADP-ribosylation (MARylation or PARylation). This PTM regulates various key biological and pathological processes. In this review, we focus on the roles of the PARP family members in inflammation and host-pathogen interactions. Here we give an overview the current understanding of the mechanisms by which PARPs promote or suppress proinflammatory activation of macrophages, and various roles PARPs play in virus infections. We also demonstrate how innovative technologies, such as proteomics and systems biology, help to advance this research field and describe unanswered questions.
Subject(s)
ADP-Ribosylation/physiology , Host-Pathogen Interactions/physiology , Inflammation , Poly(ADP-ribose) Polymerases/metabolism , Humans , Macrophages/pathology , Proteomics , Research/trends , Systems Biology , Virus Diseases/physiopathologyABSTRACT
CDTa, an actin ADP-ribosylation transferase, is a binary toxin produced by the bacterium Clostridium difficile which is commonly associated with the hypervirulent strain present in Clostridium difficile infections. The mutated form of CDTa, 4mCDTa, is one of the components in the tetravalent Clostridium difficile vaccine in which the residual toxicity of the ADP-ribosylation activity needs to be monitored for safety reasons. There are several ADP- ribosylation activity methods employing techniques such as ELISA, manual Western blot, or SDS PAGE, but all these methods are usually time consuming and labor intensive. Here we describe the development of new quantitative capillary based western for monitoring the presence of ADP-ribosylation activity in CDTa and 4mCDTa using novel, automated Simple Western™ technology. Furthermore, we have measured for the first time the enzyme's kinetic parameters, KM (NAD) and kcat for native CDTa using this new quantitative capillary western technology.
Subject(s)
ADP Ribose Transferases/genetics , Bacterial Proteins/genetics , Blotting, Western , Clostridioides difficile/enzymology , ADP-Ribosylation/physiologyABSTRACT
The transfer of adenosine diphosphate (ADP)-ribose unit(s) from nicotinamide adenine dinucleotide (NAD+) to acceptor proteins is known as ADP-ribosylation. This post-translational modification (PTM) unavoidably alters protein functions and signaling networks, thereby impacting cell behaviors and tissue outcomes. As a ubiquitous mechanism, ADP-ribosylation affects multiple tissues, including bones, as abnormal ADP-ribosylation compromises bone development and remodeling. In this review, we describe the effects of ADP-ribosylation in bone development and maintenance, and highlight the underlying mechanisms.