Poly(ADP-ribose)polymerase activity controls plant growth by promoting leaf cell number

Cajal bodies: Evolutionarily conserved nuclear biomolecular condensates with properties unique to plants

Proper orchestration of the thousands of biochemical processes that are essential to the life of every cell requires highly organized cellular compartmentalization of dedicated microenvironments. There are 2 ways to create this intracellular segregation to optimize cellular function. One way is to create specific organelles, enclosed spaces bounded by lipid membranes that regulate macromolecular flux in and out of the compartment. A second way is via membraneless biomolecular condensates that form due to to liquid-liquid phase separation. Although research on these membraneless condensates has historically been performed using animal and fungal systems, recent studies have explored basic principles governing the assembly, properties, and functions of membraneless compartments in plants. In this review, we discuss how phase separation is involved in a variety of key processes occurring in Cajal bodies (CBs), a type of biomolecular condensate found in nuclei. These processes include RNA metabolism, formation of ribonucleoproteins involved in transcription, RNA splicing, ribosome biogenesis, and telomere maintenance. Besides these primary roles of CBs, we discuss unique plant-specific functions of CBs in RNA-based regulatory pathways such as nonsense-mediated mRNA decay, mRNA retention, and RNA silencing. Finally, we summarize recent progress and discuss the functions of CBs in responses to pathogen attacks and abiotic stresses, responses that may be regulated via mechanisms governed by polyADP-ribosylation. Thus, plant CBs are emerging as highly complex and multifunctional biomolecular condensates that are involved in a surprisingly diverse range of molecular mechanisms that we are just beginning to appreciate.

Past accomplishments and future challenges of the multi-omics characterization of leaf growth

The advent of omics technologies has revolutionized biology and advanced our understanding of all biological processes, including major developmental transitions in plants and animals. Here, we review the vast knowledge accumulated concerning leaf growth in terms of transcriptional regulation before turning our attention to the historically less well-characterized alterations at the protein and metabolite level. We will then discuss how the advent of biochemical methods coupled with metabolomics and proteomics can provide insight into the protein-protein and protein-metabolite interactome of the growing leaves. We finally highlight the substantial challenges in detection, spatial resolution, integration, and functional validation of the omics results, focusing on metabolomics as a prerequisite for a comprehensive understanding of small-molecule regulation of plant growth.

Genetic loci associated with freezing tolerance in a European rapeseed (Brassica napus L.) diversity panel identified by genome-wide association mapping

Winter biotypes of rapeseed (Brassica napus L.) require a vernalization treatment to enter the reproductive phase and generally produce greater yields than spring rapeseed. To find genetic loci associated with freezing tolerance in rapeseed, we first performed genotyping-by-sequencing (GBS) on a diversity panel consisting of 222 rapeseed accessions originating primarily from Europe, which identified 69,554 high-quality single-nucleotide polymorphisms (SNPs). Model-based cluster analysis suggested that there were eight subgroups. The diversity panel was then phenotyped for freezing survival (visual damage and Fv/Fo and Fv/Fm) after 2 months of cold acclimation (5°C) and a freezing treatment (-15°C for 4 h). The genotypic and phenotypic data for each accession in the rapeseed diversity panel was then used to conduct a genome-wide association study (GWAS). GWAS results showed that 14 significant markers were mapped to seven chromosomes for the phenotypes scored. Twenty-four candidate genes located within the mapped loci were identified as previously associated with lipid, photosynthesis, flowering, ubiquitination, and cytochrome P450 in rapeseed or other plant species.

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

BACKGROUND

Poly (ADP-ribosyl) ation (PARylation) is an important posttranslational modification that regulates DNA repair, gene transcription, stress responses and developmental processes in multicellular organisms. Poly (ADP-ribose) polymerase (PARP) catalyzes PARylation by consecutively adding ADP-ribose moieties from NAD⁺ to the amino acid receptor residues on target proteins. Arabidopsis has three canonical PARP members, and two of these members, AtPARP1 and AtPARP2, have been demonstrated to be bona fide poly (ADP-ribose) polymerases and to regulate DNA repair and stress response processes. However, it remains unknown whether AtPARP3, a member that is highly expressed in seeds, has similar biochemical activity to that of AtPARP1 and AtPARP2. Additionally, although both the phylogenetic relationships and structural similarities indicate that AtPARP1 and AtPARP2 correspond to animal PARP1 and PARP2, respectively, two previous studies have indicated that AtPARP2, and not AtPARP1, accounts for most of the PARP activity in Arabidopsis, which is contrary to the knowledge that PARP1 is the predominant PARP in animals.

RESULTS

In this study, we obtained both in vitro and in vivo evidence demonstrating that AtPARP3 does not act as a typical PARP in Arabidopsis. Domain swapping and point mutation assays indicated that AtPARP3 has lost NAD⁺-binding capability and is inactive. In addition, our results showed that AtPARP1 was responsible for most of the PARP enzymatic activity in response to the DNA damage-inducing agents zeocin and methyl methanesulfonate (MMS) and was more rapidly activated than AtPARP2, which supports that AtPARP1 remains the predominant PARP member in Arabidopsis. AtPARP1 might first become activated by binding to damaged sites, and AtPARP2 is then poly (ADP-ribosyl) ated by AtPARP1 in vivo.

CONCLUSIONS

Collectively, our biochemical and genetic analysis results strongly support the notion that AtPARP3 has lost poly (ADP-ribose) polymerase activity in plants and performs different functions from those of AtPARP1 and AtPARP2. AtPARP1, instead of AtPARP2, plays the predominant role in PAR synthesis in both seeds and seedlings. These data bring new insights into our understanding of the physiological functions of plant PARP family members.

Mutation of Mediator subunit CDK8 counteracts the stunted growth and salicylic acid hyperaccumulation phenotypes of an Arabidopsis MED5 mutant

The Mediator complex functions as a hub for transcriptional regulation. MED5, an Arabidopsis Mediator tail subunit, is required for maintaining phenylpropanoid homeostasis. A semidominant mutation (ref4-3) that causes a single amino acid substitution in MED5b functions as a strong suppressor of the pathway, leading to decreased soluble phenylpropanoid accumulation, reduced lignin content and dwarfism. By contrast, loss of MED5 results in increased concentrations of phenylpropanoids. We used a reverse genetic approach to identify suppressors of ref4-3 and found that ref4-3 requires CDK8, a kinase module subunit of Mediator, to repress plant growth. The genetic interaction between MED5 and CDK8 was further characterized using mRNA-sequencing (RNA-seq) and metabolite analysis. Growth inhibition and suppression of phenylpropanoid metabolism can be genetically separated in ref4-3 by elimination of CDK8 kinase activity; however, the stunted growth of ref4-3 is not dependent on the phosphorylation event introduced by the G383S mutation. In addition, rather than perturbation of lignin biosynthesis, misregulation of DJC66, a gene encoding a DNAJ protein, is involved in the dwarfism of the med5 mutants. Together, our study reveals genetic interactions between Mediator tail and kinase module subunits and enhances our understanding of dwarfing in phenylpropanoid pathway mutants.

Abnormal leaf development of rpt5a mutant under zinc deficiency reveals important role of DNA damage alleviation for normal leaf development

Leaf development in plants, including dorsoventral (adaxial–abaxial) patterning, is tightly regulated. The involvement of several subunits of the 26S proteasome in adaxial–abaxial polarity establishment has been reported. In the present study, we revealed that in Arabidopsis thaliana, a mutation in RPT5A, a subunit of 26S proteasome, causes abnormally narrow true leaves under zinc deficiency. mRNA accumulations of DNA damage marker genes in leaves were elevated by zinc deficiency. PARP2, a single-strand break (SSB) inducible gene, was more strongly induced by zinc deficiency in rpt5a mutants compared with the wild type. A comet assay indicated that SSB is enhanced in mutants grown under the zinc deficiency condition. These results suggest that SSB accumulation is accompanied by abnormal leaf development. To test if DNA damage is a sole cause of abnormal leaf development, we treated the wild type grown under normal zinc conditions with zeocin, a DNA damage-inducing reagent, and found that narrow leaves developed, suggesting that DNA damage is sufficient to induce the development of abnormally narrow leaves. Taken together with the observation of the abnormal leaf morphology of our mutant plant under zinc deficiency, we demonstrated that the alleviation of DNA damage is important for normal leaf development.

Poly(ADP-Ribose) Polymerases in Plants and Their Human Counterparts: Parallels and Peculiarities

Poly(ADP-ribosyl)ation is a rapid and transient post-translational protein modification that was described first in mammalian cells. Activated by the sensing of DNA strand breaks, poly(ADP-ribose)polymerase1 (PARP1) transfers ADP-ribose units onto itself and other target proteins using NAD⁺ as a substrate. Subsequently, DNA damage responses and other cellular responses are initiated. In plants, poly(ADP-ribose) polymerases (PARPs) have also been implicated in responses to DNA damage. The Arabidopsis genome contains three canonical PARP genes, the nomenclature of which has been uncoordinated in the past. Albeit assumptions concerning the function and roles of PARP proteins in planta have often been inferred from homology and structural conservation between plant PARPs and their mammalian counterparts, plant-specific roles have become apparent. In particular, PARPs have been linked to stress responses of plants. A negative role under abiotic stress has been inferred from studies in which a genetic or, more commonly, pharmacological inhibition of PARP activity improved the performance of stressed plants; in response to pathogen-associated molecular patterns, a positive role has been suggested. However, reports have been inconsistent, and the effects of PARP inhibitors appear to be more robust than the genetic abolition of PARP gene expression, indicating the presence of alternative targets of those drugs. Collectively, recent evidence suggests a conditionality of stress-related phenotypes of parp mutants and calls for a reconsideration of PARP inhibitor studies on plants. This review critically summarizes our current understanding of poly(ADP-ribosylation) and PARP proteins in plants, highlighting similarities and differences to human PARPs, areas of controversy, and requirements for future studies.

The Multiple Functions of the Nucleolus in Plant Development, Disease and Stress Responses

The nucleolus is the most conspicuous domain in the eukaryotic cell nucleus, whose main function is ribosomal RNA (rRNA) synthesis and ribosome biogenesis. However, there is growing evidence that the nucleolus is also implicated in many other aspects of cell biology, such as regulation of cell cycle, growth and development, senescence, telomerase activity, gene silencing, responses to biotic and abiotic stresses. In the first part of the review, we briefly assess the traditional roles of the plant nucleolus in rRNA synthesis and ribosome biogenesis as well as possible functions in other RNA regulatory pathways such as splicing, nonsense-mediated mRNA decay and RNA silencing. In the second part of the review we summarize recent progress and discuss already known and new hypothetical roles of the nucleolus in plant growth and development. In addition, this part will highlight studies showing new nucleolar functions involved in responses to pathogen attack and abiotic stress. Cross-talk between the nucleolus and Cajal bodies is also discussed in the context of their association with poly(ADP ribose)polymerase (PARP), which is known to play a crucial role in various physiological processes including growth, development and responses to biotic and abiotic stresses.

Nicotinamide; antioxidative and DNA hypomethylation effects in plant cells

The effects of nicotinamide (NIC) and its natural plant metabolites nicotinic acid (NIA) and trigonelline (TRIG) were studied with respect to defense in plant cell cultures. NIC and NIA could protect against oxidative stress damage caused by 2,2'-azobis(2-amidinopropane) dihydrochloride (AAPH), which generates free radicals. Damage was analyzed as DNA strand breaks in cell cultures of Pisum sativum (garden pea), Daucus carota (carrot), Populus tremula L. × P. tremuloides (hybrid aspen) and Catharanthus roseus (Madagascar periwinkle), monitored by single cell gel electrophoresis (comet assay), and assays of cell leakage in C. roseus. The activities of aconitase and fumarase enzymes, which have key roles in energy metabolism, were analyzed in P. sativum cultures after treatment with NIC or NIA. Aconitase activity was increased by NIA, and fumarase activity was increased by both compounds. These compounds were shown to promote glutathione metabolism in P. sativum cultures, and NIC was shown to have a global DNA hypomethylating effect. Neither TRIG nor poly(ADP-ribose) polymerase (PARP) inhibitor 3-aminobenzamide offered any protection against DNA damage or cell leakage, nor did they promote aconitase or fumarase activities, or glutathione metabolism. By this broad approach addressing multiple biochemical factors and different plant species, we demonstrate that NIC and NIA protect plant cells from oxidative stress, and that NIC clearly exerts an epigenetic effect; decreased DNA methylation. This indicates that these compounds have important roles in the regulation of metabolism in plant cells, especially in connection to stress.

Linkage mapping aided by de novo genome and transcriptome assembly in Portunus trituberculatus: applications in growth-related QTL and gene identification

A high-resolution genetic linkage map is an essential tool for decoding genetics and genomics in non-model organisms. In this study, a linkage map was constructed for the swimming crab (Portunus trituberculatus) with 10,963 markers; as far as we know, this number of markers has never been achieved in any other crustacean. The linkage map covered 98.85% of the whole genome with a mean marker interval of 0.51 cM. The de novo assembly based on genome and transcriptome sequencing data enabled 2,378 explicit annotated markers to be anchored to the map. Quantitative trait locus (QTL) mapping revealed 10 growth-related QTLs with a phenotypic variance explained (PVE) range of 12.0-35.9. Eight genes identified from the growth-related QTL regions, in particular, RE1-silencing transcription factor and RNA-directed DNA polymerase genes with nonsynonymous substitutions, were considered important growth-related candidate genes. We have demonstrated that linkage mapping aided by de novo assembly of genome and transcriptome sequencing could serve as an important platform for QTL mapping and the identification of trait-related genes.

Poly(ADP-ribose) polymerases regulate cell division and development in Arabidopsis roots

Root organogenesis involves cell division, differentiation and expansion. The molecular mechanisms regulating root development are not fully understood. In this study, we identified poly(adenosine diphosphate (ADP)-ribose) polymerases (PARPs) as new players in root development. PARP catalyzes poly(ADP-ribosyl)ation of proteins by repeatedly adding ADP-ribose units onto proteins using nicotinamide adenine dinucleotide (NAD⁺ ) as the donor. We found that inhibition of PARP activities by 3-aminobenzomide (3-AB) increased the growth rates of both primary and lateral roots, leading to a more developed root system. The double mutant of Arabidopsis PARPs, parp1parp2, showed more rapid primary and lateral root growth. Cyclin genes regulating G1-to-S and G2-to-M transition were up-regulated upon treatment by 3-AB. The proportion of 2C cells increased while cells with higher DNA ploidy declined in the roots of treated plants, resulting in an enlarged root meristematic zone. The expression level of PARP2 was very low in the meristematic zone but high in the maturation zone, consistent with a role of PARP in inhibiting mitosis and promoting cell differentiation. Our results suggest that PARPs play an important role in root development by negatively regulating root cell division.

Cajal bodies and their role in plant stress and disease responses

Cajal bodies (CBs) are distinct sub-nuclear structures that are present in eukaryotic living cells and are often associated with the nucleolus. CBs play important roles in RNA metabolism and formation of RNPs involved in transcription, splicing, ribosome biogenesis, and telomere maintenance. Besides these primary roles, CBs appear to be involved in additional functions that may not be directly related to RNA metabolism and RNP biogenesis. In this review, we assess possible roles of plant CBs in RNA regulatory pathways such as nonsense-mediated mRNA decay and RNA silencing. We also summarize recent progress and discuss new non-canonical functions of plant CBs in responses to stress and disease. It is hypothesized that CBs can regulate these responses via their interaction with poly(ADP ribose)polymerase (PARP), which is known to play an important role in various physiological processes including responses to biotic and abiotic stresses. It is suggested that CBs and their components modify PARP activities and functions.

Analysis of knockout mutants reveals non-redundant functions of poly(ADP-ribose)polymerase isoforms in Arabidopsis

The enzyme poly(ADP-ribose)polymerase (PARP) has a dual function being involved both in the poly(ADP-ribosyl)ation and being a constituent of the NAD(+) salvage pathway. To date most studies, both in plant and non-plant systems, have focused on the signaling role of PARP in poly(ADP-ribosyl)ation rather than any role that can be ascribed to its metabolic function. In order to address this question we here used a combination of expression, transcript and protein localization studies of all three PARP isoforms of Arabidopsis alongside physiological analysis of the corresponding mutants. Our analyses indicated that whilst all isoforms of PARP were localized to the nucleus they are also present in non-nuclear locations with parp1 and parp3 also localised in the cytosol, and parp2 also present in the mitochondria. We next isolated and characterized insertional knockout mutants of all three isoforms confirming a complete knockout in the full length transcript levels of the target genes as well as a reduced total leaf NAD hydrolase activity in the two isoforms (PARP1, PARP2) that are highly expressed in leaves. Physiological evaluation of the mutant lines revealed that they displayed distinctive metabolic and root growth characteristics albeit unaltered leaf morphology under optimal growth conditions. We therefore conclude that the PARP isoforms play non-redundant non-nuclear metabolic roles and that their function is highly important in rapidly growing tissues such as the shoot apical meristem, roots and seeds.

Arabidopsis PARG1 is the key factor promoting cell survival among the enzymes regulating post-translational poly(ADP-ribosyl)ation

Poly(ADP-ribosyl)ation is a reversible post-translational modification of proteins, characterized by the addition of poly(ADP-ribose) (PAR) to proteins by poly(ADP-ribose) polymerase (PARP), and removal of PAR by poly(ADP-ribose) glycohydrolase (PARG). Three PARPs and two PARGs have been found in Arabidopsis, but their respective roles are not fully understood. In this study, the functions of each PARP and PARG in DNA repair were analyzed based on their mutant phenotypes under genotoxic stresses. Double or triple mutant analysis revealed that PARP1 and PARP2, but not PARP3, play a similar but not critical role in DNA repair in Arabidopsis seedlings. PARG1 and PARG2 play an essential and a minor role, respectively under the same conditions. Mutation of PARG1 results in increased DNA damage level and enhanced cell death in plants after bleomycin treatment. PARG1 expression is induced primarily in root and shoot meristems by bleomycin and induction of PARG1 is dependent on ATM and ATR kinases. PARG1 also antagonistically modulates the DNA repair process by preventing the over-induction of DNA repair genes. Our study determined the contribution of each PARP and PARG member in DNA repair and indicated that PARG1 plays a critical role in this process.

Natures balancing act: examining biosynthesis de novo, recycling and processing damaged vitamin B metabolites

Plants use B vitamin compounds as cofactors for metabolism. Biosynthesis de novo of these metabolites in plants is almost fully elucidated. However, salvaging of precursors as well as cofactor derivatives is only being unraveled. Furthermore, processing of these compounds when damaged by cellular activities to prevent deleterious effects on metabolism is emerging. Recent investigations indicate that the role of B vitamins goes beyond metabolism and are being linked with epigenetic traits, specific developmental cues, the circadian clock, as well as abiotic and biotic stress responses. More in depth investigations on the regulation of the provision of these compounds through biosynthesis de novo, salvage and transport is suggesting that plants may share the cost of this load by division of labor.

The guard cell metabolome: functions in stomatal movement and global food security

Guard cells represent a unique single cell-type system for the study of cellular responses to abiotic and biotic perturbations that affect stomatal movement. Decades of effort through both classical physiological and functional genomics approaches have generated an enormous amount of information on the roles of individual metabolites in stomatal guard cell function and physiology. Recent application of metabolomics methods has produced a substantial amount of new information on metabolome control of stomatal movement. In conjunction with other "omics" approaches, the knowledge-base is growing to reach a systems-level description of this single cell-type. Here we summarize current knowledge of the guard cell metabolome and highlight critical metabolites that bear significant impact on future engineering and breeding efforts to generate plants/crops that are resistant to environmental challenges and produce high yield and quality products for food and energy security.

PARP2 Is the Predominant Poly(ADP-Ribose) Polymerase in Arabidopsis DNA Damage and Immune Responses

Poly (ADP-ribose) polymerases (PARPs) catalyze the transfer of multiple poly(ADP-ribose) units onto target proteins. Poly(ADP-ribosyl)ation plays a crucial role in a variety of cellular processes including, most prominently, auto-activation of PARP at sites of DNA breaks to activate DNA repair processes. In humans, PARP1 (the founding and most characterized member of the PARP family) accounts for more than 90% of overall cellular PARP activity in response to DNA damage. We have found that, in contrast with animals, in Arabidopsis thaliana PARP2 (At4g02390), rather than PARP1 (At2g31320), makes the greatest contribution to PARP activity and organismal viability in response to genotoxic stresses caused by bleomycin, mitomycin C or gamma-radiation. Plant PARP2 proteins carry SAP DNA binding motifs rather than the zinc finger domains common in plant and animal PARP1 proteins. PARP2 also makes stronger contributions than PARP1 to plant immune responses including restriction of pathogenic Pseudomonas syringae pv. tomato growth and reduction of infection-associated DNA double-strand break abundance. For poly(ADP-ribose) glycohydrolase (PARG) enzymes, we find that Arabidopsis PARG1 and not PARG2 is the major contributor to poly(ADP-ribose) removal from acceptor proteins. The activity or abundance of PARP2 is influenced by PARP1 and PARG1. PARP2 and PARP1 physically interact with each other, and with PARG1 and PARG2, suggesting relatively direct regulatory interactions among these mediators of the balance of poly(ADP-ribosyl)ation. As with plant PARP2, plant PARG proteins are also structurally distinct from their animal counterparts. Hence core aspects of plant poly(ADP-ribosyl)ation are mediated by substantially different enzymes than in animals, suggesting the likelihood of substantial differences in regulation.

Protein poly(ADP-ribosyl)ation regulates arabidopsis immune gene expression and defense responses

Perception of microbe-associated molecular patterns (MAMPs) elicits transcriptional reprogramming in hosts and activates defense to pathogen attacks. The molecular mechanisms underlying plant pattern-triggered immunity remain elusive. A genetic screen identified Arabidopsis poly(ADP-ribose) glycohydrolase 1 (atparg1) mutant with elevated immune gene expression upon multiple MAMP and pathogen treatments. Poly(ADP-ribose) glycohydrolase (PARG) is predicted to remove poly(ADP-ribose) polymers on acceptor proteins modified by poly(ADP-ribose) polymerases (PARPs) with three PARPs and two PARGs in Arabidopsis genome. AtPARP1 and AtPARP2 possess poly(ADP-ribose) polymerase activity, and the activity of AtPARP2 was enhanced by MAMP treatment. AtPARG1, but not AtPARG2, carries glycohydrolase activity in vivo and in vitro. Importantly, mutation (G450R) in atparg1 blocks its activity and the corresponding residue is highly conserved and essential for human HsPARG activity. Consistently, mutant atparp1atparp2 plants exhibited compromised immune gene activation and enhanced susceptibility to pathogen infections. Our study indicates that protein poly(ADP-ribosyl)ation plays critical roles in plant immune gene expression and defense to pathogen attacks.

Fine-tuning of gene expression is a key feature of successful immune responses. However, the underlying mechanisms are not fully understood. Through a genetic screen in model plant Arabidopsis, we reveal that protein poly(ADP-ribosyl)ation (PARylation) post-translational modification plays a pivotal role in controlling plant immune gene expression and defense to pathogen attacks. PARylation is primarily mediated by poly(ADP-ribose) polymerase (PARP), which transfers ADP-ribose moieties from NAD⁺ to acceptor proteins. The covalently attached poly(ADP-ribose) polymers on the accept proteins could be hydrolyzed by poly(ADP-ribose) glycohydrolase (PARG). We further show that members of Arabidopsis PARPs and PARGs possess differential in vivo and in vitro enzymatic activities. Importantly, the Arabidopsis parp mutant displayed reduced, whereas parg mutant displayed enhanced, immune gene activation and immunity to pathogen infection. Moreover, Arabidopsis PARP2 activity is elevated upon pathogen signal perception. Compared to the lethality of their mammalian counterparts, the viability and normal growth of Arabidopsis parp and parg null mutants provide a unique genetic system to understand protein PARylation in diverse biological processes at the whole organism level.