New perspectives on the plant PARP family: Arabidopsis PARP3 is inactive, and PARP1 exhibits predominant poly (ADP-ribose) polymerase activity in response to DNA damage

Regulatory and Catalytic Domains of Poly(ADP-ribose) Polymerases Cross-Complement for DNA-Break-Dependent Allosteric Stimulation of Catalytic Activity

Allosteric regulation is achieved by regulatory domains that sense stimuli and induce conformational changes in the functional domain that performs the catalytic activity of the enzyme. Poly-ADP-ribose polymerases (PARPs) are modular enzymes present across all domains of life including Archaea, Bacteria, and Eukarya. A typical domain architecture of PARPs consists of a conserved C-terminal catalytic domain (CAT) associated with multiple distinct N-terminal sensory and/or regulatory domains which together serve as regulatory region (REG). In this study, we investigated whether REG of different orthologs and paralogs of PARPs from mammals (hPARP1 and hPARP2), plants (atPARP2), and bacteria (haPARP) can assemble with CAT of each other to generate functional chimeric assemblies. We have employed qualitative and quantitative enzyme activity assays along with binding studies to examine these in vitro chimeric assemblies. The cis-complemented REG and CAT of hPARP2 exhibited micromolar binding affinity, suggesting that these domains can interact independent of allosteric ligands. Also, our results show that REG and CAT of PARP proteins can assemble in a functionally active conformation in the presence of DNA implying that REG and CAT are not required to be present on a single polypeptide for catalytic activity stimulation. Interestingly, only CAT of atPARP2 displayed functional complementation with REG of the other studied PARPs. Conversely, REG of hPARP1 and atPARP2 failed to cross-complement CAT of other PARPs while REG of hPARP2 showed robust cross-complementation. Our novel studies on chimeric PARP assemblies can be developed as a powerful synthetic biology tool to interrogate and control their activities in living cells. In addition, by co-engineering non-complementing REG and CAT domains of different PARPs, new functional chimeric PARPs can be developed for selective allosteric ligand-dependent regulation of PARP systems. Furthermore, our study can facilitate the understanding of the coevolution of REG and CAT domains in PARP enzymes.

Multi-stage structure-based virtual screening approach combining 3D pharmacophore, docking and molecular dynamic simulation towards the identification of potential selective PARP-1 inhibitors

Presently, humanity is confronted with a range of diseases that have high death rates, especially those linked to cancerous growths. Several enzymes and proteins have been discovered as highly attractive targets for cancer treatment. The PARP family consists of 17 members and plays a crucial role in repairing DNA damage, which enables the survival of cancer cells. PARP-1 and, to a lesser extent, PARP-2 display above 90% activity in response to DNA damage, thereby distinguishing them apart from other members of the PARP family. Elevated levels of PARP-1 were observed in many types of tumor cells, such as breast, lung, ovarian, prostate, and melanomas. In an attempt to provide a future guide for developing selective inhibitors for PARP-1 over PARP-2 to minimize the resulting side effects from PARP-2 inhibitors, we constructed a structure-based virtual screening approach (SBVS). Firstly. A 3D pharmacophore was constructed based on the interaction of the selective inhibitor compound IV. After that, a database of nearly 450,000 phthalimide-containing inhibitors was screened through the validated pharmacophore, and 165 compounds were retrieved. The retrieved compounds were docked into the active site of PARP-1 where only 5 compounds MWGS-1-5 achieved a favorable docking score than the reference IV (-16.8 Kcal/mol). Redocking of the five compounds should have excellent selectivity for PARP-1 over PARP-2, especially compound MWGS-1. Further endorsement via molecular dynamics has proven higher affinity and selectivity for MWGS-1 towards PARP-1 over PARP-2, in which PARP-1- MWGS-1 and PARP-1- MWGS-1 achieved RMSD values of 1.42 and 2.8 Å, respectively.

Poly(ADP-ribose) polymerase FonPARP1-catalyzed PARylation of protein disulfide isomerase FonPdi1 regulates pathogenicity of Fusarium oxysporum f. sp. niveum on watermelon

Poly(ADP-ribosyl)ation (PARylation), catalyzed by poly(ADP-ribose) polymerases (PARPs) and hydrolyzed by poly(ADP-ribose) glycohydrolase (PARG), is an important reversible post-translational protein modification in all eukaryotes, including plant pathogenic fungi. Previously, we revealed that FonPARP1, an active PARP, is crucial for the pathogenicity of Fusarium oxysporum f. sp. niveum (Fon), the causative agent of watermelon Fusarium wilt. This study explores the enzymatic activity and substrates of FonPARP1 in regulating Fon pathogenicity. FonPARP1 is localized in nuclei of Fon macroconidia and hyphae. Essential conserved domains and a key glutamic acid residue at position 729 are critical for FonPARP1 enzyme activity and pathogenicity function in Fon. FonPARP1 interacts with protein disulfide isomerase FonPdi1 and PARylates it at 13 glutamic acid residues, affecting the interaction ability, PDI activity, ER homeostasis, and pathogenicity function. FonPARG1, interacting with both FonPARP1 and FonPdi1, hydrolyzes poly(ADP-ribose) chains from auto-PARylated FonPARP1 and FonPARP1-PARylated FonPdi1. These findings underscore the role of FonPARP1-catalyzed PARylation in regulating Fon pathogenicity and its significance in plant pathogenic fungi.

Poly ADP-Ribosylation in a Plant Pathogenic Oomycete Phytophthora infestans: A Key Controller of Growth and Host Plant Colonisation

ADP-ribosylation is a reversible modification of proteins and nucleic acids, which controls major cellular processes, including DNA damage repair, cell proliferation and differentiation, metabolism, stress, and immunity in plants and animals. The involvement of ADP-ribosylation in the life cycle of Dictyostelium and some filamentous fungi has also been demonstrated. However, the role of this process in pathogenic oomycetes has never been addressed. Here, we show that the Phytophthora infestans genome contains two PARP-like protein genes (PiPARP1 and PiPARP2), and provide evidence of PARylation activity for one of them (PiPARP2). Using dsRNA-mediated RNA silencing of the PiPARP2 gene and chemical (pharmacological) inhibition of PARP activity by 3-aminobenzamide (3AB) PARP inhibitor, we demonstrate the critical functional role of ADP-ribosylation in Phytophthora mycelium growth. Virulence test on detached leaves also suggests an important role of ADP-ribosylation in Phytophthora host plant colonisation and pathogenesis. On a practical level, our data suggest that targeting the PARylation system may constitute a novel powerful approach for the management of Phytophthora diseases.

Disruption of Poly(ADP-ribosyl)ation Improves Plant Tolerance to Methyl Viologen-Mediated Oxidative Stress via Induction of ROS Scavenging Enzymes

ADP-ribosylation (ADPRylation) is a mechanism which post-translationally modifies proteins in eukaryotes in order to regulate a broad range of biological processes including programmed cell death, cell signaling, DNA repair, and responses to biotic and abiotic stresses. Poly(ADP-ribosyl) polymerases (PARPs) play a key role in the process of ADPRylation, which modifies target proteins by attaching ADP-ribose molecules. Here, we investigated whether and how PARP1 and PARylation modulate responses of Nicotiana benthamiana plants to methyl viologen (MV)-induced oxidative stress. It was found that the burst of reactive oxygen species (ROS), cell death, and loss of tissue viability invoked by MV in N. benthamiana leaves was significantly delayed by both the RNA silencing of the PARP1 gene and by applying the pharmacological inhibitor 3-aminobenzamide (3AB) to inhibit PARylation activity. This in turn reduced the accumulation of PARylated proteins and significantly increased the gene expression of major ROS scavenging enzymes including SOD (NbMnSOD; mitochondrial manganese SOD), CAT (NbCAT2), GR (NbGR), and APX (NbAPX5), and inhibited cell death. This mechanism may be part of a broader network that regulates plant sensitivity to oxidative stress through various genetically programmed pathways.

Redox regulation of chromatin remodelling in plants

Changes in the cellular redox balance that occur during plant responses to unfavourable environmental conditions significantly affect a myriad of redox-sensitive processes, including those that impact on the epigenetic state of the chromatin. Various epigenetic factors, like histone modifying enzymes, chromatin remodelers, and DNA methyltransferases can be targeted by oxidative posttranslational modifications. As their combined action affects the epigenetic regulation of gene expression, they form an integral part of plant responses to (a)biotic stress. Epigenetic changes triggered by unfavourable environmental conditions are intrinsically linked with primary metabolism that supplies intermediates and donors, such acetyl-CoA and S-adenosyl-methionine, that are critical for the epigenetic decoration of histones and DNA. Here, we review the recent advances in our understanding of redox regulation of chromatin remodelling, dynamics of epigenetic marks, and the interplay between epigenetic control of gene expression, redox signalling and primary metabolism within an (a)biotic stress context.

Specific and shared biological functions of PARP2 - is PARP2 really a lil' brother of PARP1?

PARP2, that belongs to the family of ADP-ribosyl transferase enzymes (ART), is a discovery of the millennium, as it was identified in 1999. Although PARP2 was described initially as a DNA repair factor, it is now evident that PARP2 partakes in the regulation or execution of multiple biological processes as inflammation, carcinogenesis and cancer progression, metabolism or oxidative stress-related diseases. Hereby, we review the involvement of PARP2 in these processes with the aim of understanding which processes are specific for PARP2, but not for other members of the ART family. A better understanding of the specific functions of PARP2 in all of these biological processes is crucial for the development of new PARP-centred selective therapies.

Phthalimide-tethered isatins as novel poly(ADP-ribose) polymerase inhibitors: Design, synthesis, biological evaluations, and molecular modeling investigations

Humanity is currently facing various diseases with significant mortality rates, particularly those associated with malignancies. Numerous enzymes and proteins have been identified as highly promising targets for the treatment of cancer. The poly(ADP-ribose) polymerases (PARPs) family comprises 17 members which are essential in DNA damage repair, allowing the survival of cancer cells. Unlike other PARP family members, PARP-1 and, to a lesser extent, PARP-2 show more than 90% activity in response to DNA damage. PARP-1 levels were shown to be elevated in various tumor cells, including breast, lung, ovarian, and prostate cancer and melanomas. Accordingly, novel series of phthalimide-tethered isatins (6a-n, 10a-e, and 11a-e) were synthesized as potential PARP-1 inhibitors endowed with anticancer activity. All the synthesized molecules were assessed against PARP-1, where compounds 6f and 10d showed nanomolar activities with IC50  = 15.56 ± 2.85 and 13.65 ± 1.42 nM, respectively. Also, the assessment of the antiproliferative effects of the synthesized isatins was conducted on four cancer cell lines: leukemia (K-562), liver (HepG2), and breast (MCF-7 and HCC1937) cancers. Superiorly, compounds 6f and 10d demonstrated submicromolar IC50 values against breast cancer MCF-7 (IC50  = 0.92 ± 0.18 and 0.67 ± 0.12 µM, respectively) and HCC1937 (IC50  = 0.88 ± 0.52 and 0.53 ± 0.11 µM, respectively) cell lines. In addition, compounds 6f and 10d induced arrest in the G2/M phase of the cell cycle as compared to untreated cells. Finally, in silico studies, including docking and molecular dynamic simulations, were performed to justify the biological results.

Aging-Induced Reduction in Safflower Seed Germination via Impaired Energy Metabolism and Genetic Integrity Is Partially Restored by Sucrose and DA-6 Treatment

Seed storage underpins global agriculture and the seed trade and revealing the mechanisms of seed aging is essential for enhancing seed longevity management. Safflower is a multipurpose oil crop, rich in unsaturated fatty acids that are at high risk of peroxidation as a contributory factor to seed aging. However, the molecular mechanisms responsible for safflower seed viability loss are not yet elucidated. We used controlled deterioration (CDT) conditions of 60% relative humidity and 50 °C to reduce germination in freshly harvested safflower seeds and analyzed aged seeds using biochemical and molecular techniques. While seed malondialdehyde (MDA) and fatty acid content increased significantly during CDT, catalase activity and soluble sugar content decreased. KEGG analysis of gene function and qPCR validation indicated that aging severely impaired several key functional and biosynthetic pathways including glycolysis, fatty acid metabolism, antioxidant activity, and DNA replication and repair. Furthermore, exogenous sucrose and diethyl aminoethyl hexanoate (DA-6) treatment partially promoted germination in aged seeds, further demonstrating the vital role of impaired sugar and fatty acid metabolism during the aging and recovery processes. We concluded that energy metabolism and genetic integrity are impaired during aging, which contributes to the loss of seed vigor. Such energy metabolic pathways as glycolysis, fatty acid degradation, and the tricarboxylic acid cycle (TCA) are impaired, especially fatty acids produced by the hydrolysis of triacylglycerols during aging, as they are not efficiently converted to sucrose via the glyoxylate cycle to provide energy supply for safflower seed germination and seedling growth. At the same time, the reduced capacity for nucleotide synthesis capacity and the deterioration of DNA repair ability further aggravate the damage to DNA, reducing seed vitality.

Base Excision DNA Repair in Plants: Arabidopsis and Beyond

Base excision DNA repair (BER) is a key pathway safeguarding the genome of all living organisms from damage caused by both intrinsic and environmental factors. Most present knowledge about BER comes from studies of human cells, E. coli, and yeast. Plants may be under an even heavier DNA damage threat from abiotic stress, reactive oxygen species leaking from the photosynthetic system, and reactive secondary metabolites. In general, BER in plant species is similar to that in humans and model organisms, but several important details are specific to plants. Here, we review the current state of knowledge about BER in plants, with special attention paid to its unique features, such as the existence of active epigenetic demethylation based on the BER machinery, the unexplained diversity of alkylation damage repair enzymes, and the differences in the processing of abasic sites that appear either spontaneously or are generated as BER intermediates. Understanding the biochemistry of plant DNA repair, especially in species other than the Arabidopsis model, is important for future efforts to develop new crop varieties.

Effect of postharvest nicotinamide treatment on NAD+ metabolism and redox status in strawberry fruit during storage

The increased activity of PARP enzymes is associated with a deficiency of NAD+, as well as with a loss of NADPH and ATP, and consequent deterioration of the redox state in fruits. In this study, we checked whether treatment with nicotinamide (NAM) would affect PARP-1 expression and NAD+ metabolism in strawberry fruit during storage. For this purpose, strawberry fruits were treated with 10 mM NAM and co-treated with NAM and UV-C, and then stored for 5 days at 4 °C. Research showed that nicotinamide contributes to reducing oxidative stress level by reducing PARP-1 mRNA gene expression and the protein level resulting in higher NAD+ availability, as well as improving energy metabolism and NADPH levels in fruits, regardless of whether they are exposed to UV-C. The above effects cause fruits treated with nicotinamide to be characterised by higher anti-radical activity, and a lower level of reactive oxygen species in the tissue.

Plant Poly(ADP-Ribose) Polymerase 1 Is a Potential Mediator of Cross-Talk between the Cajal Body Protein Coilin and Salicylic Acid-Mediated Antiviral Defence

The nucleolus and Cajal bodies (CBs) are sub-nuclear domains with well-known roles in RNA metabolism and RNA-protein assembly. However, they also participate in other important aspects of cell functioning. This study uncovers a previously unrecognised mechanism by which these bodies and their components regulate host defences against pathogen attack. We show that the CB protein coilin interacts with poly(ADP-ribose) polymerase 1 (PARP1), redistributes it to the nucleolus and modifies its function, and that these events are accompanied by substantial increases in endogenous concentrations of salicylic acid (SA), activation of SA-responsive gene expression and callose deposition leading to the restriction of tobacco rattle virus (TRV) systemic infection. Consistent with this, we also find that treatment with SA subverts the negative effect of the pharmacological PARP inhibitor 3-aminobenzamide (3AB) on plant recovery from TRV infection. Our results suggest that PARP1 could act as a key molecular actuator in the regulatory network which integrates coilin activities as a stress sensor for virus infection and SA-mediated antivirus defence.

ADP-Ribosylation and Antiviral Resistance in Plants

ADP-ribosylation (ADPRylation) is a versatile posttranslational modification in eukaryotic cells which is involved in the regulation of a wide range of key biological processes, including DNA repair, cell signalling, programmed cell death, growth and development and responses to biotic and abiotic stresses. Members of the poly(ADP-ribosyl) polymerase (PARP) family play a central role in the process of ADPRylation. Protein targets can be modified by adding either a single ADP-ribose moiety (mono(ADP-ribosyl)ation; MARylation), which is catalysed by mono(ADP-ribosyl) transferases (MARTs or PARP "monoenzymes"), or targets may be decorated with chains of multiple ADP-ribose moieties (PARylation), via the activities of PARP "polyenzymes". Studies have revealed crosstalk between PARylation (and to a lesser extent, MARylation) processes in plants and plant-virus interactions, suggesting that these tight links may represent a novel factor regulating plant antiviral immunity. From this perspective, we go through the literature linking PARylation-associated processes with other plant regulation pathways controlling virus resistance. Once unraveled, these links may serve as the basis of innovative strategies to improve crop resistance to viruses under challenging environmental conditions which could mitigate yield losses.

The superior salinity tolerance of bread wheat cultivar Shanrong No. 3 is unlikely to be caused by elevated Ta-sro1 poly-(ADP-ribose) polymerase activity

Structural and biochemical analyses demonstrate that the elevated salinity tolerance of bread wheat cultivar Shanrong No. 3 is unlikely to be caused by elevated Ta-sro1 poly(ADP-ribose) polymerase activity.

Ozonation process causes changes in PARP-1 expression and the metabolism of NADPH in strawberry fruit during storage

In this study, the effect of ozonation process on the poly(ADP-ribose) polymerase 1 gene expression (PARP-1) and related the NADPH metabolism in strawberry fruit during storage was determined. Our results showed that ozonation with gas at both 10 and 100 ppm concentrations increased the expression of PARP-1 in the fruit during storage. Furthermore, the ozonation process initially increased the level of NAD⁺ and NADH in the fruit, which corresponds to a higher ATP level. The storage of the fruit in an ozone atmosphere also contributed to increased activity of the NAD⁺ kinase, leading to increased levels of NADP⁺ . In turn, the higher activity of glucose-6-phosphate dehydrogenase caused the ozonated fruit to show a higher level of NADPH. However, as the storage period extended and thus with increasing expression of PARP-1 in the ozonated fruit, the level of NAD⁺ decreased. In general, the ozonated fruit, which had a higher level of NADPH, showed a higher content of reduced glutathione, which in turn contributed to an increase in the antioxidant activity of the fruit and, ultimately, to a lower accumulation of reactive oxygen species.

Impact of Exogenous Application of Potato Virus Y-Specific dsRNA on RNA Interference, Pattern-Triggered Immunity and Poly(ADP-ribose) Metabolism

In this work we developed and exploited a spray-induced gene silencing (SIGS)-based approach to deliver double-stranded RNA (dsRNA), which was found to protect potato against potato virus Y (PVY) infection. Given that dsRNA can act as a defence-inducing signal that can trigger sequence-specific RNA interference (RNAi) and non-specific pattern-triggered immunity (PTI), we suspected that these two pathways may be invoked via exogeneous application of dsRNA, which may account for the alterations in PVY susceptibility in dsRNA-treated potato plants. Therefore, we tested the impact of exogenously applied PVY-derived dsRNA on both these layers of defence (RNAi and PTI) and explored its effect on accumulation of a homologous virus (PVY) and an unrelated virus (potato virus X, PVX). Here, we show that application of PVY dsRNA in potato plants induced accumulation of both small interfering RNAs (siRNAs), a hallmark of RNAi, and some PTI-related gene transcripts such as WRKY29 (WRKY transcription factor 29; molecular marker of PTI), RbohD (respiratory burst oxidase homolog D), EDS5 (enhanced disease susceptibility 5), SERK3 (somatic embryogenesis receptor kinase 3) encoding brassinosteroid-insensitive 1-associated receptor kinase 1 (BAK1), and PR-1b (pathogenesis-related gene 1b). With respect to virus infections, PVY dsRNA suppressed only PVY replication but did not exhibit any effect on PVX infection in spite of the induction of PTI-like effects in the presence of PVX. Given that RNAi-mediated antiviral immunity acts as the major virus resistance mechanism in plants, it can be suggested that dsRNA-based PTI alone may not be strong enough to suppress virus infection. In addition to RNAi- and PTI-inducing activities, we also showed that PVY-specific dsRNA is able to upregulate production of a key enzyme involved in poly(ADP-ribose) metabolism, namely poly(ADP-ribose) glycohydrolase (PARG), which is regarded as a positive regulator of biotic stress responses. These findings offer insights for future development of innovative approaches which could integrate dsRNA-induced RNAi, PTI and modulation of poly(ADP-ribose) metabolism in a co-ordinated manner, to ensure a high level of crop protection.

Responses of genes of DNA repair, alternative oxidase, and pro-/antioxidant state in Arabidopsis thaliana with altered expression of AOX1a to gamma irradiation

PURPOSE

High doses of gamma (γ) irradiation cause oxidative stress and DNA damage. Alternative oxidase (AOX) catalyzes the energy-dissipating cyanide-resistant alternative pathway in plant mitochondria and is an important part of the cellular defense network under stress conditions. In this study, Arabidopsis thaliana plants with an altered expression of the AOX1a gene were exposed by high dose-rate ionizing radiation to assess the expression of genes of DNA repair and pro-/antioxidant states to elucidate the functional significance of AOX in plant stress response.

MATERIALS AND METHODS

Five-week-old A. thaliana plants, either with basal AOX1a gene expression (wild-type Colombia-0 (Col-0)), antisense silencing of AOX1a (AS-12), and overexpression of the gene (XX-2), were γ-irradiated at a dose of 200 Gy. Gene expression and biochemical analyses were performed 12 h after irradiation.

RESULTS

Acute γ-irradiation caused different responses between the genotypes. XX-2 plants, either control or irradiated, showed the highest expression of AOX1a gene and AOX protein, and the lowest expression of DNA repair genes. Wild type and AS-12 plants exposed to γ-irradiation upregulated another stress-induced gene, AOX1d, and DNA repair genes. Furthermore, a higher activity of Mn-dependent superoxide dismutase (Mn-SOD) was observed in the irradiated AS-12 plants than in the untreated plants of this line. However, AS-12 plants were less effective than Col-0 plants in controlling the accumulation of the superoxide anion. XX-2 plants had the lowest reactive oxygen species (ROS) levels among the genotypes.

CONCLUSIONS

AS-12 plants display a compensatory mechanism by increasing the expression of AOX1d and the synthesis of the AOX protein, as well as by Mn-SOD activation. However, these were insufficient to maintain the background level of embryonic lethal mutations, and thereby the reproductive capacity. These results highlight the importance of AOX in the successful adaptation of plants to acute γ-irradiation, and indicate that AOX1a plays a key role in the regulation of the stress response.

Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice (Oryza sativa L.)

Heavy-ion irradiation is a powerful mutagen and is widely used for mutation breeding. In this study, using whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) techniques, we comprehensively characterized these dynamic changes caused by mutations at three time points (48, 96, and 144 h after irradiation) and the expression profiles of rice seeds irradiated with C ions at two doses. Subsequent WGS analysis revealed that more mutations were detected in response to 40 Gy carbon ion beam (CIB) irradiation than 80 Gy of CIB irradiation at the initial stage (48 h post-irradiation). In the mutants generated from both irradiation doses, single-base substitutions (SBSs) were the most frequent type of mutation induced by CIB irradiation. Among the mutations, the predominant ones were C:T and A:G transitions. CIB irradiation also induced many short InDel mutations. RNA-seq analysis at the three time points showed that the number of differentially expressed genes (DEGs) was highest at 48 h post-irradiation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs showed that the "replication and repair" pathway was enriched specifically 48 h post-irradiation. These results indicate that the DNA damage response (DDR) and the mechanism of DNA repair tend to quickly start within the initial stage (48 h) after irradiation.

An Insight Into the Mechanism of Plant Organelle Genome Maintenance and Implications of Organelle Genome in Crop Improvement: An Update

Besides the nuclear genome, plants possess two small extra chromosomal genomes in mitochondria and chloroplast, respectively, which contribute a small fraction of the organelles’ proteome. Both mitochondrial and chloroplast DNA have originated endosymbiotically and most of their prokaryotic genes were either lost or transferred to the nuclear genome through endosymbiotic gene transfer during the course of evolution. Due to their immobile nature, plant nuclear and organellar genomes face continuous threat from diverse exogenous agents as well as some reactive by-products or intermediates released from various endogenous metabolic pathways. These factors eventually affect the overall plant growth and development and finally productivity. The detailed mechanism of DNA damage response and repair following accumulation of various forms of DNA lesions, including single and double-strand breaks (SSBs and DSBs) have been well documented for the nuclear genome and now it has been extended to the organelles also. Recently, it has been shown that both mitochondria and chloroplast possess a counterpart of most of the nuclear DNA damage repair pathways and share remarkable similarities with different damage repair proteins present in the nucleus. Among various repair pathways, homologous recombination (HR) is crucial for the repair as well as the evolution of organellar genomes. Along with the repair pathways, various other factors, such as the MSH1 and WHIRLY family proteins, WHY1, WHY2, and WHY3 are also known to be involved in maintaining low mutation rates and structural integrity of mitochondrial and chloroplast genome. SOG1, the central regulator in DNA damage response in plants, has also been found to mediate endoreduplication and cell-cycle progression through chloroplast to nucleus retrograde signaling in response to chloroplast genome instability. Various proteins associated with the maintenance of genome stability are targeted to both nuclear and organellar compartments, establishing communication between organelles as well as organelles and nucleus. Therefore, understanding the mechanism of DNA damage repair and inter compartmental crosstalk mechanism in various sub-cellular organelles following induction of DNA damage and identification of key components of such signaling cascades may eventually be translated into strategies for crop improvement under abiotic and genotoxic stress conditions. This review mainly highlights the current understanding as well as the importance of different aspects of organelle genome maintenance mechanisms in higher plants.

Poly ADP-ribose polymerase-1 promotes seed-setting rate by facilitating gametophyte development and meiosis in rice (Oryza sativa L.)

Poly(ADP-ribose) polymerases (PARPs), which transfer either monomer or polymer of ADP-ribose from nicotinamide adenine dinucleotide (NAD⁺ ) onto target proteins, are required for multiple processes in DNA damage repair, cell cycle, development, and abiotic stress in animals and plants. Here, the uncharacterized rice (Oryza sativa) OsPARP1, which has been predicted to have two alternative OsPARP1 mRNA splicing variants, OsPARP1.1 and OsPARP1.2, was investigated. However, bimolecular fluorescence complementation showed that only OsPARP1.1 interacted with OsPARP3 paralog, suggesting that OsPARP1.1 is a functional protein in rice. OsPARP1 was preferentially expressed in the stamen primordial and pollen grain of mature stamen during flower development. The osparp1 mutant and CRISPR plants were delayed in germination, indicating that defective DNA repair machinery impairs early seed germination. The mutant displayed a normal phenotype during vegetative growth but had a lower seed-setting rate than wild-type plants under normal conditions. Chromosome bridges and DNA fragmentations were detected in male meiocytes at anaphase I to prophase II. After meiosis II, malformed tetrads or tetrads with micronuclei were formed. Meanwhile, the abnormality was also found in embryo sac development. Collectively, these results suggest that OsPARP1 plays an important role in mediating response to DNA damage and gametophyte development, crucial for rice yield in the natural environment.

Copy number analyses of DNA repair genes reveal the role of poly(ADP-ribose) polymerase (PARP) in tree longevity

Long-lived organisms are exposed to the risk of accumulating mutations due to DNA damage. Previous studies in animals have revealed the positive relationship between the copy number of DNA repair genes and longevity. However, the role of DNA repair in the lifespan of plants remains poorly understood. Using the recent accumulation of the complete genome sequences of diverse plant species, we performed systematic comparative analyses of the copy number variations of DNA repair genes in 61 plant species with different lifespans. Among 121 DNA repair gene families, PARP gene family was identified as a unique gene that exhibits significant expansion in trees compared to annual and perennial herbs. Among three paralogs of plant PARPs, PARP1 showed a close association with growth rate. PARPs catalyze poly(ADP-ribosyl)ation and play pivotal roles in DNA repair and antipathogen defense. Our study suggests the conserved role of PARPs in longevity between plants and animals.

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Comparing the copy number variations of DNA repair genes in diverse plant species

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PARP gene family showed higher copy number in trees compared to herbs

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There was negative correlation between copy number of PARP1 and growth rate in trees

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Increased copy number of PARP would be evolutionary favored in plant longevity

The Arabidopsis thaliana Poly(ADP-Ribose) Polymerases 1 and 2 Modify DNA by ADP-Ribosylating Terminal Phosphate Residues

Proteins from the poly(ADP-ribose) polymerase (PARP) family, such as PARP1 and PARP2, use NAD⁺ as a substrate to catalyze the synthesis of polymeric chains consisting of ADP-ribose units covalently attached to an acceptor molecule. PARP1 and PARP2 are viewed as DNA damage sensors that, upon binding to strand breaks, poly(ADP-ribosyl)ate themselves and nuclear acceptor proteins. The flowering plant Arabidopsis thaliana contains three genes encoding homologs of mammalian PARPs: atPARP1, atPARP2, and atPARP3. Both atPARP1 and atPARP2 contain poly(ADP-ribosyl)ating activity; however, it is unknown whether they could covalently modify DNA by ADP-ribosylating the strand break termini. Here, we report that similar to their mammalian counterparts, the plant atPARP1 and atPARP2 proteins ADP-ribosylate 5′-terminal phosphate residues in duplex DNA oligonucleotides and plasmid containing at least two closely spaced DNA strand breaks. AtPARP1 preferentially catalyzes covalent attachment of ADP-ribose units to the ends of recessed DNA duplexes containing 5′-phosphate, whereas atPARP2 preferentially ADP-ribosylates the nicked and gapped DNA duplexes containing the terminal 5′-phosphate. Similar to their mammalian counterparts, the plant PARP-catalyzed DNA ADP-ribosylation is particularly sensitive to the distance that separates two strand breaks in the same DNA molecule, 1.5 and 1 or 2 turns of helix for atPARP1 and atPARP2, respectively. PAR glycohydrolase (PARG) restored native DNA structure by hydrolyzing the PAR–DNA adducts generated by atPARPs. Biochemical and mass spectrometry analyses of the PAR–DNA adducts showed that atPARPs utilize phosphorylated DNA termini as an alternative to protein acceptor residues to catalyze PAR chain synthesis via phosphodiester bond formation between C1′ of ADP-ribose and a phosphate residue of the terminal nucleotide in DNA fragment. Taken together, these data establish the presence of a new type of DNA-modifying activity in Arabidopsis PARPs, suggesting a possible role of DNA ADP-ribosylation in DNA damage signaling and repair of terrestrial plants.

Photo-Protective Mechanisms and the Role of Poly (ADP-Ribose) Polymerase Activity in a Facultative CAM Plant Exposed to Long-Term Water Deprivation

The Crassulacean acid metabolism (CAM) pathway helps plants to alleviate the oxidative stress under drought, but the shift to CAM-idling may expose plants to the overproduction of reactive oxygen species causing cell damages. The facultative CAM species Portulacaria afra L., was subjected to long-term water deprivation to assess the photo-protective strategies and the poly (ADP-ribose) polymerase (PARP) activity during water stress and plant capability to recover from the stress. Measurements of titratable acidity, chlorophyll fluorescence emission, and antioxidant activity were performed during the stress and rewatering. Under water deprivation, plants shifted from C3 to CAM metabolism, reaching the CAM-idling status at the end of the stress period. The daily variation of the titratable acidity and PARP activity increased at the beginning of stress and declined with stress progression, reaching the lowest value at the end of stress treatment. H₂O₂ content, superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities increased with the severity of water stress. The photochemical processes remained high during the entire stress period indicating the presence of alternative sinks to CO₂ fixation. The elevated activity of catalase under severe water stress suggests the occurrence of photorespiration in sustaining the photosynthetic electron transport under CAM-idling condition. The overall data indicate that scavenger enzymes, photorespiration and PARP activity modulation contribute to the strong resistance of P. afra to severe water stress, preserving the functioning of photosynthetic apparatus and ensuring plant recovery with rewatering.

Crosstalk between Ubiquitination and Other Post-translational Protein Modifications in Plant Immunity

Post-translational modifications (PTMs) are central to the modulation of protein activity, stability, subcellular localization, and interaction with partners. They greatly expand the diversity and functionality of the proteome and have taken the center stage as key players in regulating numerous cellular and physiological processes. Increasing evidence indicates that in addition to a single regulatory PTM, many proteins are modified by multiple different types of PTMs in an orchestrated manner to collectively modulate the biological outcome. Such PTM crosstalk creates a combinatorial explosion in the number of proteoforms in a cell and greatly improves the ability of plants to rapidly mount and fine-tune responses to different external and internal cues. While PTM crosstalk has been investigated in depth in humans, animals, and yeast, the study of interplay between different PTMs in plants is still at its infant stage. In the past decade, investigations showed that PTMs are widely involved and play critical roles in the regulation of interactions between plants and pathogens. In particular, ubiquitination has emerged as a key regulator of plant immunity. This review discusses recent studies of the crosstalk between ubiquitination and six other PTMs, i.e., phosphorylation, SUMOylation, poly(ADP-ribosyl)ation, acetylation, redox modification, and glycosylation, in the regulation of plant immunity. The two basic ways by which PTMs communicate as well as the underlying mechanisms and diverse outcomes of the PTM crosstalk in plant immunity are highlighted.