Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human disease.

ARH3/ADPRHL2 and PARG are the primary enzymes reversing ADP-ribosylation in vertebrates, yet their functions in vivo remain unclear. ARH3 is the only hydrolase able to remove serine-linked mono(ADP-ribose) (MAR) but is much less efficient than PARG against poly(ADP-ribose) (PAR) chains in vitro. Here, by using ARH3-deficient cells, we demonstrate that endogenous MARylation persists on chromatin throughout the cell cycle, including mitosis, and is surprisingly well tolerated. Conversely, persistent PARylation is highly toxic and has distinct physiological effects, in particular on active transcription histone marks such as H3K9ac and H3K27ac. Furthermore, we reveal a synthetic lethal interaction between ARH3 and PARG and identify loss of ARH3 as a mechanism of PARP inhibitor resistance, both of which can be exploited in cancer therapy. Finally, we extend our findings to neurodegeneration, suggesting that patients with inherited ARH3 deficiency suffer from stress-induced pathogenic increase in PARylation that can be mitigated by PARP inhibition.

(ADP-ribosyl)hydrolases: structure, function, and biology.

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.

Fishery management in a marine protected area with compliance gaps: Socio-economic and biological insights as a first step on the path of sustainability.

Overfishing is one of the main impacts on the marine environment and multiple-use Marine Protected Areas (MPAs) could be a useful tool to conserve biodiversity and promote sustainable resource exploitation. However, ensuring a high level of protection on the ground is a difficult task. This work contributes to the analysis of the causes at the root of MPAs' ineffectiveness by examining the management of Paracentrotus lividus fishery in an Italian MPA, employing a multidisciplinary approach built on biological and socio-economic competences. This sea urchin species has a determinant ecological role in structuring infralittoral benthic assemblages and is the most exploited echinoid in Europe. From 2010 to 2018, underwater sampling was conducted over 39 monitoring sites to define P. lividus spatial and temporal trends. Declared catches and semi-structured interviews with local stakeholders were used to define the socio-economical context, underline existing conflicts among them, as well as to trace the historical evolution of sea urchin fishery. The results show that the management of sea urchin fishery is not sustainable, primarily because of the stakeholders' non-compliance with the rules. P. lividus stock is progressively declining (-73% in 9 years), showing no difference between MPA (0.5 ± 0.15 ind./m2) and control sites (0.3 ± 0.04 ind./m2). Moreover, fishermen dominate the social arena while scientists, civil society and local press have little relevance. Additionally, the untruthfulness of catch declarations was proved, the IUU fishery is relevant and the black market is hiding the actual economic value. This work offers management solutions that may be useful in other areas that show similar compliance issues.

PARPs in genome stability and signal transduction: implications for cancer therapy.

The poly(ADP-ribose) polymerase (PARP) superfamily of enzymes catalyses the ADP-ribosylation (ADPr) of target proteins by using nicotinamide adenine dinucleotide (NAD+) as a donor. ADPr reactions occur either in the form of attachment of a single ADP-ribose nucleotide unit on target proteins or in the form of ADP-ribose chains, with the latter called poly(ADP-ribosyl)ation. PARPs regulate many cellular processes, including the maintenance of genome stability and signal transduction. In this review, we focus on the PARP family members that possess the ability to modify proteins by poly(ADP-ribosyl)ation, namely PARP1, PARP2, Tankyrase-1, and Tankyrase-2. Here, we detail the cellular functions of PARP1 and PARP2 in the regulation of DNA damage response and describe the function of Tankyrases in Wnt-mediated signal transduction. Furthermore, we discuss how the understanding of these pathways has provided some major breakthroughs in the treatment of human cancer.

Serine is a new target residue for endogenous ADP-ribosylation on histones.

ADP-ribosylation (ADPr) is a biologically and clinically important post-translational modification, but little is known about the amino acids it targets on cellular proteins. Here we present a proteomic approach for direct in vivo identification and quantification of ADPr sites on histones. We have identified 12 unique ADPr sites in human osteosarcoma cells and report serine ADPr as a new type of histone mark that responds to DNA damage.

Disruption of Macrodomain Protein SCO6735 Increases Antibiotic Production in Streptomyces coelicolor.

ADP-ribosylation is a post-translational modification that can alter the physical and chemical properties of target proteins and that controls many important cellular processes. Macrodomains are evolutionarily conserved structural domains that bind ADP-ribose derivatives and are found in proteins with diverse cellular functions. Some proteins from the macrodomain family can hydrolyze ADP-ribosylated substrates and therefore reverse this post-translational modification. Bacteria and Streptomyces, in particular, are known to utilize protein ADP-ribosylation, yet very little is known about their enzymes that synthesize and remove this modification. We have determined the crystal structure and characterized, both biochemically and functionally, the macrodomain protein SCO6735 from Streptomyces coelicolor This protein is a member of an uncharacterized subfamily of macrodomain proteins. Its crystal structure revealed a highly conserved macrodomain fold. We showed that SCO6735 possesses the ability to hydrolyze PARP-dependent protein ADP-ribosylation. Furthermore, we showed that expression of this protein is induced upon DNA damage and that deletion of this protein in S. coelicolor increases antibiotic production. Our results provide the first insights into the molecular basis of its action and impact on Streptomyces metabolism.

Processing of protein ADP-ribosylation by Nudix hydrolases.

ADP-ribosylation is a post-translational modification (PTM) of proteins found in organisms from all kingdoms of life which regulates many important biological functions including DNA repair, chromatin structure, unfolded protein response and apoptosis. Several cellular enzymes, such as macrodomain containing proteins PARG [poly(ADP-ribose) glycohydrolase] and TARG1 [terminal ADP-ribose (ADPr) protein glycohydrolase], reverse protein ADP-ribosylation. In the present study, we show that human Nudix (nucleoside diphosphate-linked moiety X)-type motif 16 (hNUDT16) represents a new enzyme class that can process protein ADP-ribosylation in vitro, converting it into ribose-5'-phosphate (R5P) tags covalently attached to the modified proteins. Furthermore, our data show that hNUDT16 enzymatic activity can be used to trim ADP-ribosylation on proteins in order to facilitate analysis of ADP-ribosylation sites on proteins by MS.

The DarT/DarG Toxin-Antitoxin ADP-Ribosylation System as a Novel Target for a Rational Design of Innovative Antimicrobial Strategies.

The chemical modification of cellular macromolecules by the transfer of ADP-ribose unit(s), known as ADP-ribosylation, is an ancient homeostatic and stress response control system. Highly conserved across the evolution, ADP-ribosyltransferases and ADP-ribosylhydrolases control ADP-ribosylation signalling and cellular responses. In addition to proteins, both prokaryotic and eukaryotic transferases can covalently link ADP-ribosylation to different conformations of nucleic acids, thus highlighting the evolutionary conservation of archaic stress response mechanisms. Here, we report several structural and functional aspects of DNA ADP-ribosylation modification controlled by the prototype DarT and DarG pair, which show ADP-ribosyltransferase and hydrolase activity, respectively. DarT/DarG is a toxin-antitoxin system conserved in many bacterial pathogens, for example in Mycobacterium tuberculosis, which regulates two clinically important processes for human health, namely, growth control and the anti-phage response. The chemical modulation of the DarT/DarG system by selective inhibitors may thus represent an exciting strategy to tackle resistance to current antimicrobial therapies.

The disruption of the CCDC6 - PP4 axis induces a BRCAness like phenotype and sensitivity to PARP inhibitors in high-grade serous ovarian carcinoma.

BACKGROUND: Treatment with PARP inhibitors (PARPi) is primarily effective against high-grade serous ovarian cancers (HGSOC) with BRCA1/2 mutations or other deficiencies in homologous recombination (HR) repair mechanisms. However, resistance to PARPi frequently develops, mostly as a result of BRCA1/2 reversion mutations. The tumour suppressor CCDC6 is involved in HR repair by regulating the PP4c phosphatase activity on γH2AX. In this work, we reported that in ovarian cancer cells, a physical or functional loss of CCDC6 results synthetic lethal with the PARP-inhibitors drugs, by affecting the HR repair. We also unravelled a role for CCDC6 as predictive marker of PARPi sensitivity in ovarian cancer, and the impact of CCDC6 downregulation in overcoming PARPi resistance in these tumours. METHODS: A panel of HGSOC cell lines (either BRCA-wild type or mutant) were treated with PARPi after CCDC6 was attenuated by silencing or by inhibiting USP7, a CCDC6-deubiquitinating enzyme, and the effects on cell survival were assessed. At the cellular and molecular levels, the processes underlying the CCDC6-dependent modification of drugs' sensitivity were examined. Patient-derived xenografts (PDXs) were immunostained for CCDC6, and the expression of the protein was analysed statistically after digital or visual means. RESULTS: HGSOC cells acquired PARPi sensitivity after CCDC6 depletion. Notably, CCDC6 downregulation restored the PARPi sensitivity in newly generated or spontaneously resistant cells containing either wild type- or mutant-BRCA2. When in an un-phosphorylated state, the CCDC6 residue threonine 427 is crucial for effective CCDC6-PP4 complex formation and PP4 sequestration, which maintains high γH2AX levels and effective HR. Remarkably, the PP4-dependent control of HR repair is influenced by the CCDC6 constitutively phosphorylated mutant T427D or by the CCDC6 loss, favouring PARPi sensitivity. As a result, the PP4 regulatory component PP4R3α showed to be essential for both the activity of the PP4 complex and the CCDC6 dependent PARPi sensitivity. It's interesting to note that immunohistochemistry revealed an intense CCDC6 protein staining in olaparib-resistant HGSOC cells and PDXs. CONCLUSIONS: Our findings suggest that the physical loss or the functional impairment of CCDC6 enhances the PP4c complex activity, which causes BRCAness and PARPi sensitivity in HGSOC cells. Moreover, CCDC6 downregulation might overcome PARPi resistance in HGSOCs, thus supporting the potential of targeting CCDC6 by USP7 inhibitors to tackle PARPi resistance.

Polymer composition assessment suggests prevalence of single-use plastics among items ingested by loggerhead sea turtles in the western mediterranean sub-region.

The ingestion of plastic is becoming a major concern for various species and particularly for marine turtles across the globe. The loggerhead sea turtle (Caretta caretta) was recently chosen by the European Commission as a bio-indicator for plastic pollution within the Mediterranean basin. We further investigated which items this key species is more prone to ingest, following the standardised Marine Strategy Framework Directive protocols. Moreover, we integrated to this protocol the Fourier Transform Infrared Spectroscopy, which allowed us to determine the polymer type of each item. We analysed samples from 226 sea turtles from 2008 to 2017 in two areas of the western Mediterranean sub-region (sensu MSFD). In the Lazio area we found a frequency of occurrence of plastic ingestion of 78.33%, while in Sardinia 41.79%. The analysis of the litter categories, among all individuals, highlights a prevalence of user-sheet (Use-She; 69.13%) and user-fragment plastics (Use-Fra; 20.84%). In addition, the polymer analysis showed a dominance of polyethylene (65.98%) and polypropylene (26.23%). As a result, by looking at other works that have investigated polymer types and items sources, we are able to infer that 77.25% of the objects ingested by the C. caretta individuals are attributable to disposable daily-life objects managed in an improper way. Therefore, C. caretta apart from being an efficient bio-indicator for plastic pollution, highlighting spatial and temporal concentration differences, it could also be used to verify the effectiveness of the Single-use Plastic Directive (EU 2019/904).

Serine ADP-ribosylation in DNA-damage response regulation.

PARP1 and PARP2 govern the DNA-damage response by catalysing the reversible post-translational modification ADP-ribosylation. During the repair of DNA lesions, PARP1 and PARP2 combine with an accessory factor HPF1, which is required for the modification of target proteins on serine residues. Although the physiological role of individual ADP-ribosylation sites is still unclear, serine ADP-ribosylation at damage sites leads to the recruitment of chromatin remodellers and repair factors to ensure efficient DNA repair. ADP-ribosylation signalling is tightly controlled by the coordinated activities of (ADP-ribosyl)glycohydrolases PARG and ARH3 that, by reversing the modification, guarantee proper kinetics of DNA repair and cell cycle re-entry. The recent advances in the structural and mechanistic understanding of ADP-ribosylation provide new insights into human physiopathology and cancer therapy.

Mono(ADP-ribosyl)ation Enzymes and NAD+ Metabolism: A Focus on Diseases and Therapeutic Perspectives.

Mono(ADP-ribose) transferases and mono(ADP-ribosyl)ating sirtuins use NAD+ to perform the mono(ADP-ribosyl)ation, a simple form of post-translational modification of proteins and, in some cases, of nucleic acids. The availability of NAD+ is a limiting step and an essential requisite for NAD+ consuming enzymes. The synthesis and degradation of NAD+, as well as the transport of its key intermediates among cell compartments, play a vital role in the maintenance of optimal NAD+ levels, which are essential for the regulation of NAD+-utilizing enzymes. In this review, we provide an overview of the current knowledge of NAD+ metabolism, highlighting the functional liaison with mono(ADP-ribosyl)ating enzymes, such as the well-known ARTD10 (also named PARP10), SIRT6, and SIRT7. To this aim, we discuss the link of these enzymes with NAD+ metabolism and chronic diseases, such as cancer, degenerative disorders and aging.

Progress and outlook in studying the substrate specificities of PARPs and related enzymes.

Despite decades of research on ADP-ribosyltransferases (ARTs) from the poly(ADP-ribose) polymerase (PARP) family, one key aspect of these enzymes - their substrate specificity - has remained unclear. Here, we briefly discuss the history of this area and, more extensively, the recent breakthroughs, including the identification of protein serine residues as a major substrate of PARP1 and PARP2 in human cells and of cysteine and tyrosine as potential targets of specific PARPs. On the molecular level, the modification of serine residues requires a composite active site formed by PARP1 or PARP2 together with a specificity-determining factor, HPF1; this represents a new paradigm not only for PARPs but generally for post-translational modification (PTM) catalysis. Additionally, we discuss the identification of DNA as a substrate of PARP1, PARP2 and PARP3, and some bacterial ARTs and the discovery of noncanonical RNA capping by several PARP family members. Together, these recent findings shed new light on PARP-mediated catalysis and caution to 'expect the unexpected' when it comes to further potential substrates.

A novel approach based on multiple fish species and water column compartments in assessing vertical microlitter distribution and composition.

The assessment of the distribution and composition of microlitter in the sea is a great challenge. Biological indicators can be an irreplaceable tool since they measure microlitter levels in their environments in a way that is virtually impossible to replicate by direct physical measurements. Furthermore, trends can provide policymakers with statistically robust analysis. We looked into the capacity of multiple fish species to describe the distribution and composition of microlitter vertically across different compartments of the water column. A total of 502 individuals from six selected species (Scomber scombrus, Oblada melanura, Spicara smaris, Boops boops, Merluccius merluccius and Mullus barbatus) were collected on the western side of Sardinia island and allocated to three compartments: surface, mid-water and bottom. The species of the surface exhibited a higher frequency of occurrence (41.89%) of microlitter ingestion, compared to those of the mid-water and bottom (19.60%; 22.58%). A significant difference in the average number of ingested microlitter was found between the surface and the bottom compartment. All the microlitter fragments found were analysed through Fourier Transform Infrared Spectroscopy (FTIR). The comparison of the expected buoyancies of the polymers identified puth faith in the allocation of the species to the respective compartments. Therefore, considering the Marine Strategy Framework Directive objective, this approach could be useful in assessing microlitter distribution and composition vertically across the water column.

Spatial variability and influence of biological parameters on microplastic ingestion by Boops boops (L.) along the Italian coasts (Western Mediterranean Sea).

Recently, many studies focus on the ingestion of microplastics by marine biota. Fish exploit almost every kind of marine environment, occupy many ecological niches and are an important food source for human populations worldwide. For these reasons, they seem to represent very appropriate biological indicators of microplastic ingestion. UNEP/MAP SPA/RAC (2018) identified the bogue, Boops boops (Linnaeus, 1758), as a possible target species for monitoring microplastic ingestion in fish populations. This study provides the first report of microplastic ingestion by B. boops from the Tyrrhenian and the Ligurian Seas (Western Mediterranean Sea). Generalized Linear Mixed Models were used to analyse the relationship among biological parameters and environmental factors. A total of 379 bogues were collected in three Italian regions, subject to different anthropogenic pressures (river input, human population, shipping lanes and distance from the coast). Microplastics were detected in the gastrointestinal tract of most individuals (56%) with a mean of 1.8 (±0.2) microplastics per individual. Our study further confirms that this species is able to highlight differences in the ingestion of microplastics according to local anthropization, resulting Latium region to be the most polluted. Fish with lower physical condition are more likely to ingest microplastics, suggesting a relationship with the level of local environmental contamination. Finally, the ingestion of microplastics might be influenced by behavioural differences between sexes. According to our results, males ingest significantly more microplastics than females (p < 0.05). Our research confirms that an extensive knowledge on the biology of a bioindicator species is a priority for developing a valid monitoring strategy, such as the Marine Strategy Framework Directive for European waters.

Using Boops boops (osteichthyes) to assess microplastic ingestion in the Mediterranean Sea.

This study assesses microplastic ingestion in Boops boops at different geographical areas in the Mediterranean Sea. A total of 884 fish were caught at 20 coastal sites in Spain, France, Italy and Greece and analyzed using a common methodological protocol. Microplastics were found in 46.8% of the sampled fish, with an average number of items per individual of 1.17 ± 0.07. Filaments were the predominant shape type, while polyethylene and polypropylene were indicated by FTIR as the most common polymer types of ingested microplastics. The frequency of occurrence, as well as the abundance and proportion of types (size, shape, color and polymer) of ingested microplastics, varied among geographical areas. The spatial heterogeneity of the abundance of ingested microplastics was mainly related to the degree of coastal anthropogenic pressure at the sampling sites. Our findings further support the suitability of B. boops as bioindicator of microplastic pollution in the Mediterranean Sea.

Targeting ADP-ribosylation as an antimicrobial strategy.

ADP-ribosylation (ADPr) is an ancient reversible modification of cellular macromolecules controlling major biological processes as diverse as DNA damage repair, transcriptional regulation, intracellular transport, immune and stress responses, cell survival and proliferation. Furthermore, enzymatic reactions of ADPr are central in the pathogenesis of many human diseases, including infectious conditions. By providing a review of ADPr signalling in bacterial systems, we highlight the relevance of this chemical modification in the pathogenesis of human diseases depending on host-pathogen interactions. The post-antibiotic era has raised the need to find alternative approaches to antibiotic administration, as major pathogens becoming resistant to antibiotics. An in-depth understanding of ADPr reactions provides the rationale for designing novel antimicrobial strategies for treatment of infectious diseases. In addition, the understanding of mechanisms of ADPr by bacterial virulence factors offers important hints to improve our knowledge on cellular processes regulated by eukaryotic homologous enzymes, which are often involved in the pathogenesis of human diseases.

ADP-ribosylation signalling and human disease.

ADP-ribosylation (ADPr) is a reversible post-translational modification of proteins, which controls major cellular and biological processes, including DNA damage repair, cell proliferation and differentiation, metabolism, stress and immune responses. In order to maintain the cellular homeostasis, diverse ADP-ribosyl transferases and hydrolases are involved in the fine-tuning of ADPr systems. The control of ADPr network is vital, and dysregulation of enzymes involved in the regulation of ADPr signalling has been linked to a number of inherited and acquired human diseases, such as several neurological disorders and in cancer. Conversely, the therapeutic manipulation of ADPr has been shown to ameliorate several disorders in both human and animal models. These include cardiovascular, inflammatory, autoimmune and neurological disorders. Herein, we summarize the recent findings in the field of ADPr, which support the impact of this modification in human pathophysiology and highlight the curative potential of targeting ADPr for translational and molecular medicine.

PARPs and PAR as novel pharmacological targets for the treatment of stress granule-associated disorders.

Among the post-translational modifications, ADP-ribosylation has been for long time the least integrated in the scheme of the structural protein modifications affecting physiological functions. In spite of the original findings on bacterial-dependent ADP-ribosylation catalysed by toxins such as cholera and pertussis toxin, only with the discovery of the poly-ADP-ribosyl polymerase (PARP) family the field has finally expanded and the role of ADP-ribosylation has been recognised in both physiological and pathological processes, including cancer, infectious and neurodegenerative diseases. This is now a rapidly expanding field of investigation, centred on the role of the different PARPs and their substrates in various diseases, and on the potential of PARP inhibitors as novel pharmacological tools to be employed in relevant pathological context. In this review we analyse the role that members of the PARP family and poly-ADP-ribose (PAR; the product of PARP1 and PARP5a activity) play in the processes following the exposure of cells to different stresses. The cell response that arises following conditions such as heat, osmotic, oxidative stresses or viral infection relies on the formation of stress granules, which are transient cytoplasmic membrane-less structures, that include untranslated mRNA, specific proteins and PAR, this last one serving as the "collector" of all components (that bind to it in a non-covalent manner). The resulting phenotypes are cells in which translation, intracellular transport or pro-apoptotic pathways are reversibly inhibited, for the time the given stress holds. Interestingly, the formation of defective stress granules has been detected in diverse pathological conditions including neurological disorders and cancer. Analysing the molecular details of stress granule formation under these conditions offers a novel view on the pathogenesis of these diseases and, as a consequence, the possibility of identifying novel drug targets for their treatment.

Microplastics uptake and egestion dynamics in Pacific oysters, Magallana gigas (Thunberg, 1793), under controlled conditions.

Microplastics debris (<5 mm) are increasingly abundant in the marine environment, therefore, potentially becoming a growing threat for different marine organisms. Through aquatic animals, these can enter in the human food chain, and can be perceived as a risk for consumers' health. Different studies report the presence of particles in marketable shellfish including the world wide commercially grown Pacific oyster Magallana gigas (Thunberg, 1793). The aim of this study is to examine the potential risk of microplastics entering in the human food chain through this shellfish species, investigating the dynamics of the uptake, egestion (faeces) and rejection (pseudofaeces) of microplastics in Pacific oysters under controlled conditions. M. gigas collected from a farm in the San Teodoro lagoon (Italy), were exposed to 60 fluorescent orange polystyrene particles L-1 of known sizes (100, 250 and 500 µm). The uptake of each particle size was 19.4 ±â€¯1.1%, 19.4 ±â€¯2% and 12.9 ±â€¯2% respectively. After exposure M. gigas were left to depurate for 72 h, during which 84.6 ±â€¯2% of the particles taken up were released whilst 15.4 ±â€¯2% were retained inside the shell cavity. No microplastic particles were found in the animals' soft tissues. The results of this study, suggest that depuration is an effective method to reduce presence of large microplastic particles, in the size range 100-500 µm, in M. gigas. Importantly, the data suggests that the burden that could theoretically be up taken by consumers from these shellfish is negligible when compared to other routes.