DNA DAMAGE AND REPAIR IN PLANTS

The photoreactivation of 6 - 4 photoproducts in chloroplast and nuclear DNA depends on the amount of the Arabidopsis UV repair defective 3 protein

BACKGROUND

6 - 4 photoproducts are the second most common UV-induced DNA lesions after cyclobutane pyrimidine dimers. In plants, they are mainly repaired by photolyases in a process called photoreactivation. While pyrimidine dimers can be deleterious, leading to mutagenesis or even cell death, 6 - 4 photoproducts can activate specific signaling pathways. Therefore, their removal is particularly important, especially for plants exposed to high UV intensities due to their sessile nature. Although photoreactivation in nuclear DNA is well-known, its role in plant organelles remains unclear. In this paper we analyzed the activity and localization of GFP-tagged AtUVR3, the 6 - 4 photoproduct specific photolyase.

RESULTS

Using transgenic Arabidopsis with different expression levels of AtUVR3, we confirmed a positive trend between these levels and the rate of 6 - 4 photoproduct removal under blue light. Measurements of 6 - 4 photoproduct levels in chloroplast and nuclear DNA of wild type, photolyase mutants, and transgenic plants overexpressing AtUVR3 showed that the photoreactivation is the main repair pathway responsible for the removal of these lesions in both organelles. The GFP-tagged AtUVR3 was predominantly located in nuclei with a small fraction present in chloroplasts and mitochondria of transgenic Arabidopsis thaliana and Nicotiana tabacum lines. In chloroplasts, this photolyase co-localized with the nucleoid marked by plastid envelope DNA binding protein.

CONCLUSIONS

Photolyases are mainly localized in plant nuclei, with only a small fraction present in chloroplasts and mitochondria. Despite this unbalanced distribution, photoreactivation is the primary mechanism responsible for the removal of 6 - 4 photoproducts from nuclear and chloroplast DNA in adult leaves. The amount of the AtUVR3 photolyase is the limiting factor influencing the photoreactivation rate of 6 - 4 photoproducts. The efficient photoreactivation of 6 - 4 photoproducts in 35S: AtUVR3-GFP Arabidopsis and Nicotiana tabacum is a promising starting point to evaluate whether transgenic crops overproducing this photolyase are more tolerant to high UV irradiation and how they respond to other abiotic and biotic stresses under field conditions.

How Histone Acetyltransferases Shape Plant Photomorphogenesis and UV Response

Higher plants have developed complex mechanisms to adapt to fluctuating environmental conditions with light playing a vital role in photosynthesis and influencing various developmental processes, including photomorphogenesis. Exposure to ultraviolet (UV) radiation can cause cellular damage, necessitating effective DNA repair mechanisms. Histone acetyltransferases (HATs) play a crucial role in regulating chromatin structure and gene expression, thereby contributing to the repair mechanisms. HATs facilitate chromatin relaxation, enabling transcriptional activation necessary for plant development and stress responses. The intricate relationship between HATs, light signaling pathways and chromatin dynamics has been increasingly understood, providing valuable insights into plant adaptability. This review explores the role of HATs in plant photomorphogenesis, chromatin remodeling and gene regulation, highlighting the importance of chromatin modifications in plant responses to light and various stressors. It emphasizes the need for further research on individual HAT family members and their interactions with other epigenetic factors. Advanced genomic approaches and genome-editing technologies offer promising avenues for enhancing crop resilience and productivity through targeted manipulation of HAT activities. Understanding these mechanisms is essential for developing strategies to improve plant growth and stress tolerance, contributing to sustainable agriculture in the face of a changing climate.

An insight into the roles of ubiquitin-specific proteases in plants: development and growth, morphogenesis, and stress response

Ubiquitination is a highly conserved and dynamic post-translational modification in which protein substrates are modified by ubiquitin to influence their activity, localization, or stability. Deubiquitination enzymes (DUBs) counter ubiquitin signaling by removing ubiquitin from the substrates. Ubiquitin-specific proteases (UBPs), the largest subfamily of DUBs, are conserved in plants, serving diverse functions across various cellular processes, although members within the same group often exhibit functional redundancy. Here, we briefly review recent advances in understanding the biological roles of UBPs, particularly the molecular mechanism by which UBPs regulate plant development and growth, morphogenesis, and stress response, which sheds light on the mechanistic roles of deubiquitination in plants.

Weaker photosynthetic acclimation to fluctuating than to corresponding steady UVB radiation treatments in grapevines

The effects of transient increases in UVB radiation on plants are not well known; whether cumulative damage dominates or, alternately, an increase in photoprotection and recovery periods ameliorates any negative effects. We investigated photosynthetic capacity and metabolite accumulation of grapevines (Vitis vinifera Cabernet Sauvignon) in response to UVB fluctuations under four treatments: fluctuating UVB (FUV) and steady UVB radiation (SUV) at similar total biologically effective UVB dose (2.12 and 2.23 kJ m-2 day-1), and their two respective no UVB controls. We found a greater decrease in stomatal conductance under SUV than FUV. There was no decrease in maximum yield of photosystem II (Fv/Fm) or its operational efficiency (ɸPSII) under the two UVB treatments, and Fv/Fm was higher under SUV than FUV. Photosynthetic capacity was enhanced under FUV in the light-limited region of rapid light-response curves but enhanced by SUV in the light-saturated region. Flavonol content was similarly increased by both UVB treatments. We conclude that, while both FUV and SUV effectively stimulate acclimation to UVB radiation at realistic doses, FUV confers weaker acclimation than SUV. This implies that recovery periods between transient increases in UVB radiation reduce UVB acclimation, compared to an equivalent dose of UVB provided continuously. Thus, caution is needed in interpreting the findings of experiments using steady UVB radiation treatments to infer effects in natural environments, as the stimulatory effect of steady UVB is greater than that of the equivalent fluctuating UVB.

Poaceae plants transfer cyclobutane pyrimidine dimer photolyase to chloroplasts for ultraviolet-B resistance

Photoreactivation enzyme that repairs cyclobutane pyrimidine dimer (CPD) induced by ultraviolet-B radiation, commonly called CPD photolyase (PHR) is essential for plants living under sunlight. Rice (Oryza sativa) PHR (OsPHR) is a unique triple-targeting protein. The signal sequences required for its translocation to the nucleus or mitochondria are located in the C-terminal region but have yet to be identified for chloroplasts. Here, we identified sequences located in the N-terminal region, including the serine-phosphorylation site at position 7 of OsPHR, and found that OsPHR is transported/localized to chloroplasts via a vesicle transport system under the control of serine-phosphorylation. However, the sequence identified in this study is only conserved in some Poaceae species, and in many other plants, PHR is not localized to the chloroplasts. Therefore, we reasoned that Poaceae species need the ability to repair CPD in the chloroplast genome to survive under sunlight and have uniquely acquired this mechanism for PHR chloroplast translocation.

Deficiency of both classical and alternative end-joining pathways leads to a synergistic defect in double-strand break repair but not to an increase in homology-dependent gene targeting in Arabidopsis

In eukaryotes, double-strand breaks (DSBs) are either repaired by homologous recombination (HR) or non-homologous end-joining (NHEJ). In somatic plant cells, HR is very inefficient. Therefore, the vast majority of DSBs are repaired by two different pathways of NHEJ. The classical (cNHEJ) pathway depends on the heterodimer KU70/KU80, while polymerase theta (POLQ) is central to the alternative (aNHEJ) pathway. Surprisingly, Arabidopsis plants are viable, even when both pathways are impaired. However, they exhibit severe growth retardation and reduced fertility. Analysis of mitotic anaphases indicates that the double mutant is characterized by a dramatic increase in chromosome fragmentation due to defective DSB repair. In contrast to the single mutants, the double mutant was found to be highly sensitive to the DSB-inducing genotoxin bleomycin. Thus, both pathways can complement for each other efficiently in DSB repair. We speculated that in the absence of both NHEJ pathways, HR might be enhanced. This would be especially attractive for gene targeting (GT) in which predefined changes are introduced using a homologous template. Unexpectedly, the polq single mutant as well as the double mutant showed significantly lower GT frequencies in comparison to wildtype plants. Accordingly, we were able to show that elimination of both NHEJ pathways does not pose an attractive approach for Agrobacterium-mediated GT. However, our results clearly indicate that a loss of cNHEJ leads to an increase in GT frequency, which is especially drastic and attractive for practical applications, in which the in planta GT strategy is used.

The recent possible strategies for breeding ultraviolet-B-resistant crops

The sensitivity of crops to ultraviolet B (UVB, 280-315 nm) radiation varies significantly. Plants' sensitivity to UVB is heavily influenced by the activity of the enzyme cyclobutane pyrimidine dimer (CPD) photolyase, which fixes UVB-induced CPDs. Crops grown in tropical areas with high level of UVB radiation, like O. glaberrima from Africa and O. sativa ssp. indica rice from Bengal, are more sensitive to UVB radiation and could suffer more as a result of rising UVB levels on the earth's surface. Therefore, creating crops that can withstand high UVB is crucial in tropical regions. There is, however, little information on current techniques for breeding UVB-resistant plants. The most recent techniques for producing UVB-resistant crops are presented in this review. The use of DNA methylation, boosting the antioxidant system, regulating the expression of micro-RNA396, and overexpressing CPD photolyase in transgenic plants are some of the methods that are discussed. CPD photolyase overexpression in transgenic plants is the most popular technique for producing UVB-resistant rice. The study also offers several strategies for creating UVB-resistant plants using gene editing techniques. To feed the world's rapidly expanding population, researchers can use the information from this study to improve food production.

Effect of microplastics on urban wastewater disinfection and impact on effluent reuse: Sunlight/H2O2 vs solar photo-Fenton at neutral pH

The interference of three types of microplastics (MPs) on the inactivation of Escherichia coli (E. coli) by advanced oxidation processes (AOPs) (namely, sunlight/H2O2 and solar photo-Fenton (SPF) with Ethylenediamine-N,N'-disuccinic acid (EDDS)), in real secondary treated urban wastewater was investigated for the first time. Inactivation by sunlight/H2O2 treatment decreased as MPs concentration and H2O2 dose were increased. Noteworthy, an opposite behaviour was observed for SPF process where inactivation increased as MPs concentration was increased. Biofilm formation and microbial attachment on surfaces of post-treated MPs were observed on polyethylene (PE) and polyvinyl chloride (PVC) MPs by field emission scanning electron microscopy. In presence of PE MPs, a complete inactivation of E. Coli was achieved by SPF with EDDS (Fe:EDDS = 1:2) after 90 min treatment unlike of sunlight/H2O2 treatment (∼4.0 log reduction, 40 mg/L H2O2 dose, 90 min treatment). The lower efficiency of sunlight/H2O2 process could be attributed to the blocking/scattering effect of MPs on sunlight, which finally reduced the intracellular photo Fenton effect. A reduced E. coli regrowth was observed in presence of MPs. SPF (Fe:EDDS = 1:1) with PE MPs was less effective in controlling bacterial regrowth (∼120 CFU/100 mL) than sunlight/H2O2 (∼10 CFU/100 mL) after 48 h of post-treatment. These results provide useful information about possible interference of MPs on urban wastewater disinfection by solar driven AOPs and possible implications for effluent reuse.

Impact of ultraviolet-B radiation on early-season morpho-physiological traits of indica and japonica rice genotypes

Ultraviolet (UV)-B radiation is considered one of the major detrimental rays coming from the Sun. UV-B radiation has a harmful impact on plant growth and development. The effect of UV-B radiation was studied on 64 rice (Oryza sativa L.) genotypes during the vegetative season. An equal number of genotypes from the japonica (50%) and indica (50%) subspecies were phenotyped using the Soil-Plant-Atmosphere-Research (SPAR) units. The 10 kJ UV-B was imposed 12 days after planting (DAP) and continued for three weeks (21 d). Based on the combined ultraviolet-B radiation response index (CUVBRI) for each genotype, the 64 rice genotypes were classified into sensitive, moderately sensitive, moderately tolerant, and tolerant. Various shoot traits, such as plant height, tiller, and leaf numbers, were measured. We also studied critical root phenological traits like root volume, diameter, tips, and forks. Out of all the studied shoot traits, leaf area showed maximum reduction for both indica (54%) and japonica (48%). Among the root traits, root length decreased by negligible (1%) for indica as compared to japonica (5%), while root crossing and forks showed a maximum decline for japonica (37 and 42%), respectively. This study is timely, meaningful, and required because it will help breeders select a tolerant or sensitive rice line for better yield and production under abiotic stresses.

UV-C LED-induced cyclobutane pyrimidine dimer formation, lesion repair and mutagenesis in the biofilm-forming diatom, Navicula incerta

The use of ultraviolet-C (UV-C) irradiation in marine biofouling control is a relatively new and potentially disruptive technology. This study examined effects of UV-C exposure on the biofilm-forming diatom, Navicula incerta. UV-C-induced mutations were identified via Illumina HiSeq. A de novo genome was assembled from control sequences and reads from UV-C-exposed treatments were mapped to this genome, with a quantitative estimate of mutagenesis then derived from the frequency of single nucleotide polymorphisms. UV-C exposure increased cyclobutane pyrimidine dimer (CPD) abundance with a direct correlation between lesion formation and fluency. Cellular repair mechanisms gradually reduced CPDs over time, with the highest UV-C fluence treatments having the fastest repair rates. Mutation abundances were, however, negatively correlated with CPD abundance suggesting that UV-C exposure may influence lesion repair. The threshold fluence for CPD formation exceeding CPD repair was >1.27 J cm-2. Fluences >2.54 J cm-2 were predicted to inhibit repair mechanisms. While UV-C holds considerable promise for marine antifouling, diatoms are just one, albeit an important, component of marine biofouling communities. Determining fluence thresholds for other representative taxa, highlighting the most resistant, would allow UV-C treatments to be specifically tuned to target biofouling organisms, whilst limiting environmental effects and the power requirement.

The recent relationship between ultraviolet-B radiation and biotic resistance in plants: a novel non-chemical strategy for managing biotic stresses

Ultraviolet-B radiation (UVB; 280-315 nm) is a significant environmental factor that alters plant development, changes interactions between species, and reduces the prevalence of pests and diseases. While UVB radiation has negative effects on plant growth and performance at higher doses, at lower and ambient doses, UVB radiation acts as a non-chemical method for managing biotic stresses by having positive effects on disease resistance and genes that protect plants from pests. Understanding the recent relationship between UVB radiation and plants' biotic stresses is crucial for the development of crops that are resistant to UVB and biotic stresses. However, little is known about the recent interactions between UVB radiation and biotic stresses in plants. This review discusses the most recent connections between UVB radiation and biotic stresses in crops, including how UVB radiation affects a plant's resistance to disease and pests. The interaction of UVB radiation with pathogens and herbivores has been the subject of the most extensive research of these. This review also discusses additional potential strategies for conferring multiple UVB-biotic stress resistance in crop plants, such as controlling growth inhibition, miRNA 396 and 398 modulations, and MAP kinase. This study provides crucial knowledge and methods for scientists looking to develop multiple resistant crops that will improve global food security.

Physiological and omics-based insights for underpinning the molecular regulation of secondary metabolite production in medicinal plants: UV stress resilience

Despite complex phytoconstituents, the commercial potential of medicinal plants under ultraviolet (UV) stress environment hasn't been fully comprehended. Due to sessile nature, these plants are constantly exposed to damaging radiation, which disturbs their natural physiological and biochemical processes. To combat with UV stress, plants synthesized several small organic molecules (natural products of low molecular mass like alkaloids, terpenoids, flavonoids and phenolics, etc.) known as plant secondary metabolites (PSMs) that come into play to counteract the adverse effect of stress. Plants adapted a stress response by organizing the expression of several genes, enzymes, transcription factors, and proteins involved in the synthesis of chemical substances and by making the signaling cascade (a series of chemical reactions induced by a stimulus within a biological cell) flexible to boost the defensive response. To neutralize UV exposure, secondary metabolites and their signaling network regulate cellular processes at the molecular level. Conventional breeding methods are time-consuming and difficult to reveal the molecular pattern of the stress tolerance medicinal plants. Acquiring in-depth knowledge of the molecular drivers behind the defensive mechanism of medicinal plants against UV radiation would yield advantages (economical and biological) that will bring prosperity to the burgeoning world's population. Thus, this review article emphasized the comprehensive information and clues to identify several potential genes, transcription factors (TFs), proteins, biosynthetic pathways, and biological networks which are involved in resilience mechanism under UV stress in medicinal plants of high-altitudes.

Integrative Transcriptomics Data Mining to Explore the Functions of TDP1α and TDP1β Genes in the Arabidopsis thaliana Model Plant

The tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme hydrolyzes the phosphodiester bond between a tyrosine residue and the 3'-phosphate of DNA in the DNA-topoisomerase I (TopI) complex, being involved in different DNA repair pathways. A small TDP1 gene subfamily is present in plants, where TDP1α has been linked to genome stability maintenance, while TDP1β has unknown functions. This work aimed to comparatively investigate the function of the TDP1 genes by taking advantage of the rich transcriptomics databases available for the Arabidopsis thaliana model plant. A data mining approach was carried out to collect information regarding gene expression in different tissues, genetic backgrounds, and stress conditions, using platforms where RNA-seq and microarray data are deposited. The gathered data allowed us to distinguish between common and divergent functions of the two genes. Namely, TDP1β seems to be involved in root development and associated with gibberellin and brassinosteroid phytohormones, whereas TDP1α is more responsive to light and abscisic acid. During stress conditions, both genes are highly responsive to biotic and abiotic treatments in a time- and stress-dependent manner. Data validation using gamma-ray treatments applied to Arabidopsis seedlings indicated the accumulation of DNA damage and extensive cell death associated with the observed changes in the TDP1 genes expression profiles.

Stress Management in Plants: Examining Provisional and Unique Dose-Dependent Responses

The purpose of this review is to critically evaluate the effects of different stress factors on higher plants, with particular attention given to the typical and unique dose-dependent responses that are essential for plant growth and development. Specifically, this review highlights the impact of stress on genome instability, including DNA damage and the molecular, physiological, and biochemical mechanisms that generate these effects. We provide an overview of the current understanding of predictable and unique dose-dependent trends in plant survival when exposed to low or high doses of stress. Understanding both the negative and positive impacts of stress responses, including genome instability, can provide insights into how plants react to different levels of stress, yielding more accurate predictions of their behavior in the natural environment. Applying the acquired knowledge can lead to improved crop productivity and potential development of more resilient plant varieties, ensuring a sustainable food source for the rapidly growing global population.

Opportunities and challenges with CRISPR-Cas mediated homologous recombination based precise editing in plants and animals

We summarise recent advancements to achieve higher homologous recombination based gene targeting efficiency in different animals and plants. The genome editing has revolutionized the agriculture and human therapeutic sectors by its ability to create precise, stable and predictable mutations in the genome. It depends upon targeted double-strand breaks induction by the engineered endonucleases, which then gets repaired by highly conserved endogenous DNA repair mechanisms. The repairing could be done either through non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathways. The HDR-based editing can be applied for precise gene targeting such as insertion of a new gene, gene replacement and altering of the regulatory sequence of a gene to control the existing protein expression. However, HDR-mediated editing is considered challenging because of lower efficiency in higher eukaryotes, thus, preventing its widespread application. This article reviews the recent progress of HDR-mediated editing and discusses novel strategies such as cell cycle synchronization, modulation of DNA damage repair factors, engineering of Cas protein favoring HDR and CRISPR-Cas reagents delivery methods to improve efficiency for generating knock-in events in both plants and animals. Further, multiplexing of described methods may be promising towards achieving higher donor template-assisted homologous recombination efficiency at the target locus.

Cell death responses to acute high light mediated by non-photochemical quenching in the dinoflagellate Karenia brevis

Programmed cell death (PCD) can be induced in microalgae by many abiotic challenges via generation of reactive oxygen species (ROS). Marine phytoplankton live in a highly variable light environment, yet the potential for excess photosynthetically available radiation to trigger PCD has not been examined. On the other hand, photoprotective non-photochemical quenching (NPQ) is hypothesized to counteract intracellular ROS, potentially preventing cell death. The main objective of this study is to investigate high-light-induced death processes and their relationship with photosynthesis in bloom-forming dinoflagellate Karenia brevis. Here, we characterized the prevalence of ROS, caspase-like enzyme activity and cell death as well as photosynthetic status under acute irradiance of 500, 750 or 1000 µmol m-2 s-1. PCD only occurred at the largest light shift. Although depressed photosynthetic capacities and oxidative stress were apparent across the stress gradient, they did not necessarily lead to cell death. NPQ exhibited dose-dependent activation with increasing light stress, which enabled cells to resist or delay PCD. These results highlight the important role of the balance between ROS generation and NPQ activation on determining cell fates in Karenia under acute irradiance stress. This research also provides insights into potential survival strategies and mechanisms of cell loss under a changeable light environment.

Radiosensitivity of seedling traits to varying gamma doses, optimum dose determination and variation in determined doses due to different time of sowings after irradiation and methods of irradiation in faba bean genotypes

PURPOSE

Three experiments were conducted to assess the effect of different doses of gamma radiation on various seedling traits; determine the optimum doses of gamma radiation for different faba bean genotypes; find out the variation in optimum doses with respect to the different times of sowings after irradiation and methods of irradiation.

MATERIALS AND METHODS

Five faba bean genotypes viz., L-2013-060, L-2013-092, Anandnagar Local, Gazipur Local and Bangla Gangachar were used in these experiments. In Experiment I, seeds of five experimental genotypes were exposed to different doses (100 Gy 200 Gy, 300 Gy, 400 Gy, 500 Gy, 600 Gy, 700 Gy and 800 Gy) of gamma radiation and were sown immediately after irradiation. In Experiment II, seeds of Bangla Gangachar and L-2013-060 were exposed to varying doses (100-800 Gy) of gamma radiation and were sown at seven sowings starting from 0 h to 24 h at 4-h intervals after irradiation. In Experiment III, L-2013-092 genotypes was exposed to different doses (100 -800 Gy) of gamma radiation with two different methods of irradiation.

RESULTS

In Experiment I, the lethal dose 50 (LD₅₀) values have arrived at 140 Gy, 669 Gy, 575 Gy, 386 Gy and 158 Gy for L-2013-060, L-2013-092, Anandnagar Local, Gazipur Local and Bangla Gangachar, respectively. The growth reduction 50 (GR₅₀) doses for different seedling traits ranged from 130 Gy to 320 Gy for L-2013-060, 250 Gy to 480 Gy for L-2013-092, 130 Gy to 370 Gy for Anandnagar Local, 200 Gy to 350 Gy for Gazipur Local and 250 Gy to 400 Gy for Bangla Gangachar. In Experiment II, the values for LD₅₀ of the genotypes Bangla Gangachar and L-2013-060 were significantly singular for different time intervals of sowing. The values of GR₅₀ for most of the seedling traits were found to increase with the delay in sowing after irradiation from 4 to 24 h when compared with the immediately sown seed lots. In Experiment III, LD₅₀ for L-2013-092 was 337 Gy with Method 1 and 669 Gy with Method 2. In Method 1, most of the growth parameters attained GR₅₀ doses lower than Method 2. The first method was found to increase the radiosensitivity of L-2013-092.

CONCLUSION

Every experimental genotype used in these three experiments showed dose-dependent retardation of different seedling traits. These optimized doses may be employed to establish mutant populations for exploiting the novel traits of faba bean. The time of sowing after irradiation and method of irradiation was found to be essential for confirming optimum doses.

Growth and Biosynthesis of Phenolic Compounds of Canola (Brassica napus L.) to Different Ultraviolet (UV)-B Wavelengths in a Plant Factory with Artificial Light

The application of ultraviolet-B (UV-B) irradiation to supplement visible light as an elicitor to increase bioactive compounds under controlled conditions is increasing. This study aimed to evaluate the effects of UV-B dose and wavelength region (280−300 and 300−320 nm) on the morphological, physiological, and biochemical responses of canola plants (Brassica napus L.). Canola plants (17 days after sowing) were subjected to various UV-B intensities (i.e., 0.3, 0.6, and 0.9 W m−2) and were divided into cut and non-cut treatments for each UV treatment. Plant growth parameters exhibited different trends based on the treated UV irradiation intensity. Plant growth gradually decreased as the UV irradiation intensity and exposure time increased. Despite the same UV irradiation intensity, plant response varied significantly depending on the presence or absence of a short-wavelength cut filter (<300 nm). Canola plants suffered more leaf damage in nonfilter treatments containing shorter wavelengths (280−300 nm). UV treatment effectively activates the expression of secondary metabolite biosynthetic genes, differing depending on the UV irradiation intensity. Our results suggest that both UV irradiation intensity and wavelength should be considered when enhancing antioxidant phytochemicals without inhibiting plant growth in a plant factory with artificial light.

A Single Amino Acid Substitution in RFC4 Leads to Endoduplication and Compromised Resistance to DNA Damage in Arabidopsis thaliana

Replication factor C (RFC) is a heteropentameric ATPase associated with the diverse cellular activities (AAA+ATPase) protein complex, which is composed of one large subunit, known as RFC1, and four small subunits, RFC2/3/4/5. Among them, RFC1 and RFC3 were previously reported to mediate genomic stability and resistance to pathogens in Arabidopsis. Here, we generated a viable rfc4e (rfc4-1/RFC4^G54E) mutant with a single amino acid substitution by site-directed mutagenesis. Three of six positive T2 mutants with the same amino acid substitution, but different insertion loci, were sequenced to identify homozygotes, and the three homozygote mutants showed dwarfism, early flowering, and a partially sterile phenotype. RNA sequencing revealed that genes related to DNA repair and replication were highly upregulated. Moreover, the frequency of DNA lesions was found to be increased in rfc4e mutants. Consistent with this, the rfc4e mutants were very sensitive to DSB-inducing genotoxic agents. In addition, the G54E amino acid substitution in AtRFC4 delayed cell cycle progression and led to endoduplication. Overall, our study provides evidence supporting the notion that RFC4 plays an important role in resistance to genotoxicity and cell proliferation by regulating DNA damage repair in Arabidopsis thaliana.

A plant-specific module for homologous recombination repair

Homologous recombination repair (HR) is an error-free DNA damage repair pathway to maintain genome stability and a basis of gene targeting using genome-editing tools. However, the mechanisms of HR in plants are still poorly understood. Through genetic screens for DNA damage response mutants (DDRM) in Arabidopsis, we find that a plant-specific ubiquitin E3 ligase DDRM1 is required for HR. DDRM1 contains an N-terminal BRCT (BRCA1 C-terminal) domain and a C-terminal RING (really interesting new gene) domain and is highly conserved in plants including mosses. The ddrm1 mutant is defective in HR and thus is hypersensitive to DNA-damaging reagents. Biochemical studies reveal that DDRM1 interacts with and ubiquitinates the transcription factor SOG1, a plant-specific master regulator of DNA damage responses. Interestingly, DDRM1-mediated ubiquitination promotes the stability of SOG1. Consistently, genetic data support that SOG1 functions downstream of DDRM1. Our study reveals that DDRM1-SOG1 is a plant-specific module for HR and highlights the importance of ubiquitination in HR.

E2Fb and E2Fa transcription factors independently regulate the DNA damage response after ultraviolet B exposure in Arabidopsis

Ultraviolet (UV)B radiation affects plant growth inhibiting cell proliferation. This inhibition is in part controlled by the activity of transcription factors from the E2F family. In particular, the participation of E2Fc and E2Fe in UV-B responses in Arabidopsis plants was previously reported. However, the E2Fa and E2Fb contribution to these processes has still not been investigated. Thus, in this work, we provide evidence that, in Arabidopsis, both E2Fa and E2Fb control leaf size under UV-B conditions without participating in the repair of cyclobutane pyrimidine dimers in the DNA. Nevertheless, in UV-B-exposed seedlings, E2Fa, but not E2Fb, regulates primary root elongation, cell proliferation, and programmed cell death in the meristematic zone. Using e2fa mutants that overexpress E2Fb, we showed that the role of E2Fa in the roots could not be replaced by E2Fb. Finally, our results show that E2Fa and E2Fb differentially regulate the expression of genes that activate the DNA damage response and cell cycle progression, both under conditions without UV-B and after exposure. Overall, we showed that both E2Fa and E2Fb have different and non-redundant roles in developmental and DNA damage responses in Arabidopsis plants exposed to UV-B.

Epigenetic Mechanisms of Senescence in Plants

Senescence is a major developmental transition in plants that requires a massive reprogramming of gene expression and includes various layers of regulations. Senescence is either an age-dependent or a stress-induced process, and is under the control of complex regulatory networks that interact with each other. It has been shown that besides genetic reprogramming, which is an important aspect of plant senescence, transcription factors and higher-level mechanisms, such as epigenetic and small RNA-mediated regulators, are also key factors of senescence-related genes. Epigenetic mechanisms are an important layer of this multilevel regulatory system that change the activity of transcription factors (TFs) and play an important role in modulating the expression of senescence-related gene. They include chromatin remodeling, DNA methylation, histone modification, and the RNA-mediated control of transcription factors and genes. This review provides an overview of the known epigenetic regulation of plant senescence, which has mostly been studied in the form of leaf senescence, and it also covers what has been reported about whole-plant senescence.

UVC inactivation of pathogenic samples suitable for cryo-EM analysis

Cryo-electron microscopy has become an essential tool to understand structure and function of biological samples. Especially for pathogens, such as disease-causing bacteria and viruses, insights gained by cryo-EM can aid in developing cures. However, due to the biosafety restrictions of pathogens, samples are often treated by chemical fixation to render the pathogen inert, affecting the ultrastructure of the sample. Alternatively, researchers use in vitro or ex vivo models, which are non-pathogenic but lack the complexity of the pathogen of interest. Here we show that ultraviolet-C (UVC) radiation applied at cryogenic temperatures can be used to eliminate or dramatically reduce the infectivity of Vibrio cholerae and the bacterial virus, the ICP1 bacteriophage. We show no discernable structural impact of this treatment of either sample using two cryo-EM methods: cryo-electron tomography followed by sub-tomogram averaging, and single particle analysis (SPA). Additionally, we applied the UVC irradiation to the protein apoferritin (ApoF), which is a widely used test sample for high-resolution SPA studies. The UVC-treated ApoF sample resulted in a 2.1 Å structure indistinguishable from an untreated published map. This research demonstrates that UVC treatment is an effective and inexpensive addition to the cryo-EM sample preparation toolbox.

Depelteau et al. present a new method to inactivate cryo-EM samples from pathogenic organisms before imaging using ultraviolet-C radiation in cryogenic conditions. This method allows for the inexpensive preparation of cryo-EM samples with no discernable structural impact of the treatment.

Analysis of T-DNA integration events in transgenic rice

Agrobacterium-mediated plant transformation has been widely used for introducing transgene(s) into a plant genome and plant breeding. However, our understanding of T-DNA integration into rice genome remains limited relative to that in the model dicot Arabidopsis. To better elucidate the T-DNA integration into the rice genome, we investigated extensively the T-DNA ends and their flanking rice genomic sequences from two transgenic rice plants carrying Cowpea Trypsin Inhibitor (CpTI)-derived gene Signal-CpTI-KDEL (SCK) and Bacillus thuringiensis (BT) gene, respectively, by TAIL-PCR method. Analysis of the junction sequences between the T-DNA ends and rice genome DNA indicated that there were three joining patterns of microhomology, filler DNA sequences, and exact joining, and both the T-DNA ends tend to adopt identical manner to join the rice genome. After T-DNA integration, there were several variations of rice genomic sequences, including small deletions at the integration sites, superfluous DNA inserted between T-DNA and genome, and translocation of genomic DNA in the flanking regions. The translocation block could be from a noncontiguous region in the same chromosome or different chromosomes at the integration sites, and the originating position of the translocated block resulted in comparable deletion based on a cut/paste mechanism rather than a replication mechanism. Our study may lead to a better understand of T-DNA integration mechanism and facilitate functional genomic studies and further crop improvement.

Primary metabolic processes as drivers of leaf ageing

Ageing in plants is a highly coordinated and complex process that starts with the birth of the plant or plant organ and ends with its death. A vivid manifestation of the final stage of leaf ageing is exemplified by the autumn colours of deciduous trees. Over the past decades, technological advances have allowed plant ageing to be studied on a systems biology level, by means of multi-omics approaches. Here, we review some of these studies and argue that these provide strong support for basic metabolic processes as drivers for ageing. In particular, core cellular processes that control the metabolism of chlorophyll, amino acids, sugars, DNA and reactive oxygen species correlate with leaf ageing. However, while multi-omics studies excel at identifying correlative processes and pathways, molecular genetic approaches can provide proof that such processes and pathways control ageing, by means of knock-out and ectopic expression of predicted regulatory genes. Therefore, we also review historic and current molecular evidence to directly test the hypotheses unveiled by the systems biology approaches. We found that the molecular genetic approaches, by and large, confirm the multi-omics-derived hypotheses with notable exceptions, where there is scant evidence that chlorophyll and DNA metabolism are important drivers of leaf ageing. We present a model that summarises the core cellular processes that drive leaf ageing and propose that developmental processes are tightly linked to primary metabolism to inevitably lead to ageing and death.

Genome Maintenance Mechanisms at the Chromatin Level

Genome integrity is constantly threatened by internal and external stressors, in both animals and plants. As plants are sessile, a variety of environment stressors can damage their DNA. In the nucleus, DNA twines around histone proteins to form the higher-order structure “chromatin”. Unraveling how chromatin transforms on sensing genotoxic stress is, thus, key to understanding plant strategies to cope with fluctuating environments. In recent years, accumulating evidence in plant research has suggested that chromatin plays a crucial role in protecting DNA from genotoxic stress in three ways: (1) changes in chromatin modifications around damaged sites enhance DNA repair by providing a scaffold and/or easy access to DNA repair machinery; (2) DNA damage triggers genome-wide alterations in chromatin modifications, globally modulating gene expression required for DNA damage response, such as stem cell death, cell-cycle arrest, and an early onset of endoreplication; and (3) condensed chromatin functions as a physical barrier against genotoxic stressors to protect DNA. In this review, we highlight the chromatin-level control of genome stability and compare the regulatory systems in plants and animals to find out unique mechanisms maintaining genome integrity under genotoxic stress.

Measuring the Activity of DNA Repair Enzymes in Isolated Mitochondria

Nuclear, mitochondrial and plastidic DNA is constantly exposed to conditions, such as ultraviolet radiation or reactive oxygen species, which will induce chemical modifications to the nucleotides. Unless repaired, these modifications can lead to mutations, so the nucleus, mitochondria and plastids each contains a number of DNA repair systems. We here describe assays for measuring the enzyme activities associated with the base-excision repair pathway in potato tuber mitochondria. As the name implies, this pathway involves removing a modified base and replacing it with an undamaged base. Activity of each of the enzymes involved, DNA glycosylase, apurinic/apyrimidinic endonuclease, DNA polymerase and DNA ligase can be measured by incubating a mitochondrial extract with a specifically designed oligonucleotide. After incubation, the reaction mixture is separated on a polyacrylamide gel, and the amounts of specific products formed is estimated by autoradiography, which makes it possible to calculate the enzymatic activity.

Effects of Nocturnal UV-B Irradiation on Growth, Flowering, and Phytochemical Concentration in Leaves of Greenhouse-Grown Red Perilla

In Japan, red perilla leaves are used in the food and coloring industries, as well as in crude medicine. Perilla leaves contain a high concentration of phytochemicals such as perillaldehyde (PA) and rosmarinic acid (RA). The effects of UV-B radiation intensity (0.05–0.2 W m⁻², UV-B_BE: 0.041–0.083 W m⁻²), duration (3 or 6 h), and irradiation method (continuous or intermittent) for artificial nocturnal lighting using UV-B fluorescent lamps were evaluated on growth, flowering, and leaf phytochemical concentration in greenhouse-grown perilla. Under continuous UV-B irradiation at 0.1 W m⁻² for 3 or 6 h, leaf color changed from red to green and leaf fresh weight decreased, compared with the control treatment. No leaf color change was observed under the 3-h treatment with UV-B radiation at 0.05 W m⁻², wherein leaf fresh weight was similar to that of the control. Furthermore, RA concentration under continuous UV-B irradiation at 0.05 W m⁻² for 3 h increased two-fold compared to that under control treatment, while PA concentration was not affected by UV-B irradiation. Thus, our data showed that continuous UV-B irradiation at 0.05 W m⁻² for 3 h could effectively produce RA-rich perilla leaves without reducing in phenotypic quality or productivity. However, a 6-h intermittent illumination inhibited flowering without altering phytochemical concentration.

Chromatin dynamics during DNA damage and repair in plants: new roles for old players

The genome of plants is organized into chromatin. The chromatin structure regulates the rates of DNA metabolic processes such as replication, transcription, DNA recombination, and repair. Different aspects of plant growth and development are regulated by changes in chromatin status by the action of chromatin-remodeling activities. Recent data have also shown that many of these chromatin-associated proteins participate in different aspects of the DNA damage response, regulating DNA damage and repair, cell cycle progression, programmed cell death, and entry into the endocycle. In this review, we present different examples of proteins and chromatin-modifying enzymes with roles during DNA damage responses, demonstrating that rapid changes in chromatin structure are essential to maintain genome stability.

Slowly seeing the light: an integrative review on ecological light pollution as a potential threat for mollusks

Seasonal changes in the natural light condition play a pivotal role in the regulation of many biological processes in organisms. Disruption of this natural condition via the growing loss of darkness as a result of anthropogenic light pollution has been linked to species-wide shifts in behavioral and physiological traits. This review starts with a brief overview of the definition of light pollution and the most recent insights into the perception of light. We then go on to review the evidence for some adverse effects of ecological light pollution on different groups of animals and will focus on mollusks. Taken together, the available evidence suggests a critical role for light pollution as a recent, growing threat to the regulation of various biological processes in these animals, with the potential to disrupt ecosystem stability. The latter indicates that ecological light pollution is an environmental threat that needs to be taken seriously and requires further research attention.

UV-B Radiation Affects Photosynthesis-Related Processes of Two Italian Olea europaea (L.) Varieties Differently

Given the economical importance of the olive tree it is essential to study its responses to stress agents such as excessive UV-B radiation, to understand the defense mechanisms and to identify the varieties that are able to cope with it. In the light of the analysis carried out in this study, we argue that UV-B radiation represents a dangerous source of stress for the olive tree, especially in the current increasingly changing environmental conditions. Both the varieties considered (Giarraffa and Olivastra Seggianese), although resistant to the strong treatment to which they were exposed, showed, albeit in different ways and at different times, evident effects. The two varieties have different response times and the Giarraffa variety seems better suited to prolonged UV-B stress, possible due to a more efficient and quick activation of the antioxidant response (e.g., flavonoids use to counteract reactive oxygen species) and because of its capacity to maintain the photosynthetic efficiency as well as a relatively higher content of mannitol. Moreover, pigments reduction after a long period of UV-B exposure can also be an adaptation mechanism triggered by Giarraffa to reduce energy absorption under UV-B stress. Olivastra Seggianese seems less suited to overcome UV-B stress for a long period (e.g., higher reduction of F_v/F_m) and has a higher requirement for sugars (e.g., glucose) possible to counteract stress and to restore energy.

Expression of a Tardigrade Dsup Gene Enhances Genome Protection in Plants

DNA damage is one of the most impactful events in living organisms, leading to DNA sequence changes (mutation) and disruption of biological processes. A study has identified a protein called Damage Suppressor Protein (Dsup) in the tardigrade Ramazzotius varieornatus that has shown to reduce the effects of radiation damage in human cell cultures (Hashimoto in Nature Communications 7:12808, 2016). We have generated tobacco plants that express the codon-optimized tardigrade Dsup gene and examined their responses when treated with mutagenic chemicals, ultraviolet (UV) and ionizing radiations. Our studies showed that compared to the control plants, the Dsup-expressing plants grew better in the medium containing mutagenic ethylmethane sulfonate (EMS). RT-qPCR detected distinct expression patterns of endogenous genes involved in DNA damage response and repair in the Dsup plants in response to EMS, bleomycin, UV-C and X-ray radiations. Comet assays revealed that the nuclei from the Dsup plants appeared more protected from UV and X-ray damages than the control plants. Overall, our studies demonstrated that Dsup gene expression enhanced tolerance of plants to genomutagenic stress. We suggest the feasibility of exploring genetic resources from extremotolerant species such as tardigrades to impart plants with tolerance to stressful environments for future climate changes and human space endeavors.

Autophagy-deficient Arabidopsis mutant atg5, which shows ultraviolet-B sensitivity, cannot remove ultraviolet-B-induced fragmented mitochondria

Mitochondria damaged by ultraviolet-B radiation (UV-B, 280-315 nm) are removed by mitophagy, a selective autophagic process. Recently, we demonstrated that autophagy-deficient Arabidopsis thaliana mutants exhibit a UV-B-sensitive phenotype like that of cyclobutane pyrimidine dimer (CPD)-specific photolyase (PHR1)-deficient mutants. To explore the relationship between UV-B sensitivity and autophagy in UV-B-damaged plants, we monitored mitochondrial dynamics and autophagy in wild-type Arabidopsis (ecotype Columbia); an autophagy-deficient mutant, atg5; a PHR1-deficient mutant, phr1; an atg5 phr1 double mutant; and AtPHR1-overexpressing (AtPHR1ox) plants following high-dose UV-B exposure (1.5 W m^-2 for 1 h). At 10 h after exposure, the number of mitochondria per mesophyll leaf cell was increased and the volumes of individual mitochondria were decreased independently of UV-B-induced CPD accumulation in all genotypes. At 24 h after exposure, the mitochondrial number had recovered or almost recovered to pre-exposure levels in plants with functional autophagy (WT, phr1, and AtPHR1ox), but had increased even further in atg5. This suggested that the high dose of UV-B led to the inactivation and fragmentation of mitochondria, which were removed by mitophagy activated by UV-B. The UV-B-sensitive phenotype of the atg5 phr1 double mutant was more severe than that of atg5 or phr1. In wild-type, phr1, and AtPHR1ox plants, autophagy-related genes were strongly expressed following UV-B exposure independently of UV-B-induced CPD accumulation. Therefore, mitophagy might be one of the important repair mechanisms for UV-B-induced damage. The severe UV-B-sensitive phenotype of atg5 phr1 is likely an additive effect of deficiencies in independent machineries for UV-B protection, autophagy, and CPD photorepair.

SATMF Suppresses the Premature Senescence Phenotype of the ATM Loss-of-Function Mutant and Improves Its Fertility in Arabidopsis

Leaf senescence is the final stage of leaf development. It is accompanied by the remobilization of nutrients from senescent leaves to developing organs. The occurrence of senescence is the consequence of integrating intrinsic and environmental signals. DNA damage triggered by stresses has been regarded as one of the reasons for senescence. To prevent DNA damage, cells have evolved elaborate DNA repair machinery. The ataxia telangiectasia mutated (ATM) functions as the chief transducer of the double-strand breaks (DSBs) signal. Our previous study suggests that ATM functions in lifespan regulation in Arabidopsis. However, ATM regulatory mechanism on plant longevity remains unclear. Here, we performed chemical mutagenesis to identify the components involved in ATM-mediated longevity and obtained three dominant mutants satmf1~3, suppressor of atm in fertility, displaying delayed senescence and restored fertility in comparison with atm mutant. Molecular cloning and functional analysis of SATMF (suppressor of atm in fertility) will help to understand the underlying regulatory mechanism of ATM in plants, and shed light on developing new treatments for the disease Ataxia-telangiectasia.

Evidence for sub-functionalization of tandemly duplicated XPB nucleotide excision repair genes in Arabidopsis thaliana

Plants are continuously exposed to agents that can generate DNA lesions. Nucleotide Excision Repair (NER) is one of the repair pathways employed by plants to protect their genome, including from sunlight. The Xeroderma Pigmentosum type B (XPB) protein is a DNA helicase shown to be involved in NER and is also an essential subunitof the Transcription Factor IIH (TFIIH) complex. XPB was found to be a single copy gene in eukaryotes, but found as a tandem duplication in the plant Arabidopsis thaliana, AtXPB1 and AtXPB2. We aimed to investigate whether the XPB in tandem duplication was common within members of the Brassicaceae. We analyzed genomic DNA of species from different tribes of the family and the results indicate that the tandem duplication occurred in Camelineae tribe ancestor, of which A. thaliana belongs, at approximately 8 million years ago. Further experiments were devised to study possible functional roles for the A. thaliana AtXPB paralogs. A non-coincident expression profile of the paralogs was observed in various plant organs, developmental and cell cycle stages. AtXPB2 expression was observed in proliferating cells and clustered with the transcription of other components of the TFIIH such as p44, p52 and XPD/UVH6 along the cell cycle. AtXPB1 gene transcription, on the other hand, was enhanced specifically after UV-B irradiation in leaf trichomes. Altogether, our results reported herein suggest a functional specialization for the AtXPB paralogs: while the AtXPB2 paralog may have a role in cell proliferation and repair as XPB of other eukaryotes, the AtXPB1 paralog is most likely implicated in repair functions in highly specialized A. thaliana cells.

ATM suppresses leaf senescence triggered by DNA double-strand break through epigenetic control of senescence-associated genes in Arabidopsis

All living organisms are unavoidably exposed to various endogenous and environmental stresses that trigger potentially fatal DNA damage, including double-strand breaks (DSBs). Although a growing body of evidence indicates that DNA damage is one of the prime drivers of aging in animals, little is known regarding the importance of DNA damage and its repair on lifespan control in plants. We found that the level of DSBs increases but DNA repair efficiency decreases as Arabidopsis leaves age. Generation of DSBs by inducible expression of I-PpoI leads to premature senescence phenotypes. We examined the senescence phenotypes in the loss-of-function mutants for 13 key components of the DNA repair pathway and found that deficiency in ATAXIA TELANGIECTASIA MUTATED (ATM), the chief transducer of the DSB signal, results in premature senescence in Arabidopsis. ATM represses DSB-induced expression of senescence-associated genes, including the genes encoding the WRKY and NAC transcription factors, central components of the leaf senescence process, via modulation of histone lysine methylation. Our work highlights the significance of ATM in the control of leaf senescence and has significant implications for the conservation of aging mechanisms in animals and plants.

Space Radiation Biology for "Living in Space"

Space travel has advanced significantly over the last six decades with astronauts spending up to 6 months at the International Space Station. Nonetheless, the living environment while in outer space is extremely challenging to astronauts. In particular, exposure to space radiation represents a serious potential long-term threat to the health of astronauts because the amount of radiation exposure accumulates during their time in space. Therefore, health risks associated with exposure to space radiation are an important topic in space travel, and characterizing space radiation in detail is essential for improving the safety of space missions. In the first part of this review, we provide an overview of the space radiation environment and briefly present current and future endeavors that monitor different space radiation environments. We then present research evaluating adverse biological effects caused by exposure to various space radiation environments and how these can be reduced. We especially consider the deleterious effects on cellular DNA and how cells activate DNA repair mechanisms. The latest technologies being developed, e.g., a fluorescent ubiquitination-based cell cycle indicator, to measure real-time cell cycle progression and DNA damage caused by exposure to ultraviolet radiation are presented. Progress in examining the combined effects of microgravity and radiation to animals and plants are summarized, and our current understanding of the relationship between psychological stress and radiation is presented. Finally, we provide details about protective agents and the study of organisms that are highly resistant to radiation and how their biological mechanisms may aid developing novel technologies that alleviate biological damage caused by radiation. Future research that furthers our understanding of the effects of space radiation on human health will facilitate risk-mitigating strategies to enable long-term space and planetary exploration.

Very high sensitivity of African rice to artificial ultraviolet-B radiation caused by genotype and quantity of cyclobutane pyrimidine dimer photolyase

Ultraviolet-B (UVB) radiation damages plants and decreases their growth and productivity. We previously demonstrated that UVB sensitivity varies widely among Asian rice (Oryza sativa L.) cultivars and that the activity of cyclobutane pyrimidine dimer (CPD) photolyase, which repairs UVB-induced CPDs, determines UVB sensitivity. Unlike Asian rice, African rice (Oryza glaberrima Steud. and Oryza barthii A. Chev.) has mechanisms to adapt to African climates and to protect itself against biotic and abiotic stresses. However, information about the UVB sensitivity of African rice species is largely absent. We showed that most of the African rice cultivars examined in this study were UVB-hypersensitive or even UVB-super-hypersensitive in comparison with the UVB sensitivity of Asian O. sativa cultivars. The difference in UVB resistance correlated with the total CPD photolyase activity, which was determined by its activity and its cellular content. The UVB-super-hypersensitive cultivars had low enzyme activity caused by newly identified polymorphisms and low cellular CPD photolyase contents. The new polymorphisms were only found in cultivars from West Africa, particularly in those from countries believed to be centres of O. glaberrima domestication. This study provides new tools for improving both Asian and African rice productivity.

Flavones Produced by Mulberry Flavone Synthase Type I Constitute a Defense Line against the Ultraviolet-B Stress

Flavones, one of the largest classes of flavonoids in plants, have a variety of bioactivities and participate in the resistance response of plants to biotic and abiotic stresses. However, flavone synthase (FNS), the key enzyme for flavone biosynthesis, has not yet been characterized in mulberry. In this study, we report that the leaves of certain mulberry cultivars, namely BJ7, PS2, and G14, are rich in flavones. We identified a Fe²⁺/2-oxoglutarate-dependent dioxygenase from Morus notabilis (MnFNSI) that shows the typical enzymatic activity of a FNSI-type enzyme, and directly converts eriodictyol and naringenin into their corresponding flavones. Overexpression of MnFNSI in tobacco increased the flavones contents in leaves and enhanced the tolerance of tobacco to ultraviolet-B (UV-B) stress. We found that mulberry cultivars with higher flavones contents exhibit less UV-B induced damage after a UV-B treatment. Accordingly, our findings demonstrate that MnFNSI, a FNSI-type enzyme, is involved in the biosynthesis of flavones, which provide protection against UV-B radiation. These results lay the foundation for obtaining mulberry germplasm resources that are more tolerant to UV-B stress and richer in their nutritional value.

An insight into the mechanism of DNA damage response in plants- role of SUPPRESSOR OF GAMMA RESPONSE 1: An overview

Because of their sessile lifestyle, plants are inescapably exposed to various kinds of environmental stresses throughout their lifetime. Therefore, to regulate their growth and development, plants constantly monitor the environmental signals and respond appropriately. However, these environmental stress factors, along with some endogenous metabolites, generated in response to environmental stress factors often induce various forms of DNA damage in plants and thus promote genome instability. To maintain the genomic integrity, plants have developed an extensive, sophisticated and coordinated cellular signaling mechanism known as DNA damage response or DDR. DDR evokes a signaling process which initiates with the sensing of DNA damage and followed by the subsequent activation of downstream pathways in many directions to repair and eliminate the harmful effects of DNA damages. SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), one of the newly identified components of DDR in plant genome, appears to play central role in this signaling network. SOG1 is a member of NAC [NO APICAL MERISTEM (NAM), ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR (ATAF), CUP-SHAPED COTYLEDON (CUC)] domain family of transcription factors and involved in a diverse array of function in plants, encompassing transcriptional response to DNA damage, cell cycle checkpoint functions, ATAXIA-TELANGIECTASIA-MUTATED (ATM) or ATAXIA TELANGIECTASIA AND RAD3-RELATED (ATR) mediated activation of DNA damage response and repair, functioning in programmed cell death and regulation of induction of endoreduplication. Although most of the functional studies on SOG1 have been reported in Arabidopsis, some recent reports have indicated diverse functions of SOG1 in various other plant species, including Glycine max, Medicago truncatula, Sorghum bicolour, Oryza sativa and Zea mays, respectively. The remarkable functional diversity shown by SOG1 protein indicates its multitasking capacity. In this review, we integrate information mainly related to functional aspects of SOG1 in the context of DDR in plants. Considering the important role of SOG1 in DDR and its functional diversity, in-depth functional study of this crucial regulatory protein can provide further potential information on genome stability maintenance mechanism in plants in the context of changing environmental condition.

Blue Light Treatment but Not Green Light Treatment After Pre-exposure to UV-B Stabilizes Flavonoid Glycoside Changes and Corresponding Biological Effects in Three Different Brassicaceae Sprouts

Ultraviolet-B (UV-B; 280-315 nm) radiation induces the biosynthesis of secondary plant metabolites such as flavonoids. Flavonoids could also be enhanced by blue (420-490 nm) or green (490-585 nm) light. Flavonoids act as antioxidants and shielding components in the plant's response to UV-B exposure. They are shown to quench singlet oxygen and to be reactive to hydroxyl radical. The aim was to determine whether treatment with blue or green light can alter flavonoid profiles after pre-exposure to UV-B and whether they cause corresponding biological effects in Brassicaceae sprouts. Based on their different flavonoid profiles, three vegetables from the Brassicaceae were selected. Sprouts were treated with five subsequent doses (equals 5 days) of moderate UV-B (0.23 kJ m^-2 day^-1 UV-B_BE), which was followed with two subsequent (equals 2 days) doses of either blue (99 μmol m^-2 s^-1) or green (119 μmol m^-2 s^-1) light. In sprouts of kale, kohlrabi, and rocket salad, flavonoid glycosides were identified by HPLC-DAD-ESI-MSⁿ. Both Brassica oleracea species, kale and kohlrabi, showed mainly acylated quercetin and kaempferol glycosides. In contrast, in rocket salad, the main flavonol glycosides were quercetin glycosides. Blue light treatment after the UV-B treatment showed that quercetin and kaempferol glycosides were increased in the B. oleracea species kale and kohlrabi while-contrary to this-in rocket salad, there were only quercetin glycosides increased. Blue light treatment in general stabilized the enhanced concentrations of flavonoid glycosides while green treatment did not have this effect. Blue light treatment following the UV-B exposure resulted in a trend of increased singlet oxygen scavenging for kale and rocket. The hydroxyl radical scavenging capacity was independent from the light quality except for kale where an exposure with UV-B followed by a blue light treatment led to a higher hydroxyl radical scavenging capacity. These results underline the importance of different light qualities for the biosynthesis of reactive oxygen species that intercept secondary plant metabolites, but also show a pronounced species-dependent reaction, which is of special interest for growers.

Phosphoproteomic analysis reveals plant DNA damage signalling pathways with a functional role for histone H2AX phosphorylation in plant growth under genotoxic stress

DNA damage responses are crucial for plant growth under genotoxic stress. Accumulating evidence indicates that DNA damage responses differ between plant cell types. Here, quantitative shotgun phosphoproteomics provided high-throughput analysis of the DNA damage response network in callus cells. MS analysis revealed a wide network of highly dynamic changes in the phosphoprotein profile of genotoxin-treated cells, largely mediated by the ATAXIA TELANGIECTASIA MUTATED (ATM) protein kinase, representing candidate factors that modulate plant growth, development and DNA repair. A C-terminal dual serine target motif unique to H2AX in the plant lineage showed 171-fold phosphorylation that was absent in atm mutant lines. The physiological significance of post-translational DNA damage signalling to plant growth and survival was demonstrated using reverse genetics and complementation studies of h2ax mutants, establishing the functional role of ATM-mediated histone modification in plant growth under genotoxic stress. Our findings demonstrate the complexity and functional significance of post-translational DNA damage signalling responses in plants and establish the requirement of H2AX phosphorylation for plant survival under genotoxic stress.

Transcriptional Fidelity of Mitochondrial RNA Polymerase RpoTm from Arabidopsis thaliana

Fidelity of RNA synthesis is essential for the faithful transfer of information from DNA to RNA. A comprehensive analysis of the nucleotide selectivity by the mitochondrial RNA polymerase (RNAP) RpoTm, from Arabidopsis thaliana, has been carried out. The kinetic parameters for the incorporation of cognate, noncognate, and oxidized bases have been determined. The results establish high fidelity of mitochondrial transcription resembling those of replicative polymerases in the absence of repair. In addition, RpoTm incorporates oxidized nucleotides with similar efficiency compared with mismatches and is capable of extending the RNA beyond the insertion of the oxidized base. Furthermore, lesion bypass study on RpoTm demonstrates that the enzyme bypasses 8-oxo-guanine by insertion of adenine leading to C to A mutations in RNA. Homology modeling of RpoTm elongation complex allows delineation of the residues necessary for stabilizing the incoming NTP substrate and for posing the template nucleotide residue. Substitution of these residues leads to compromise in the activity of the enzyme corroborating their importance in RNA synthesis. Comparison of the data with T7 RNAPs indicates that low efficiency of misincorporation is a universal strategy used by single-subunit RNAPs for maintaining high fidelity in the absence of proofreading and repair activity in mitochondria.

AtCAF-1 mutants show different DNA damage responses after ultraviolet-B than those activated by other genotoxic agents in leaves

Chromatin assembly factor-1 (CAF-1) is a histone H3/H4 chaperone that participates in DNA and chromatin interaction processes. In this manuscript, we show that organs from CAF-1 deficient plants respond differently to ultraviolet-B (UV-B) radiation than to other genotoxic stresses. For example, CAF-1 deficient leaves tolerate better UV-B radiation, showing lower cyclobutane pyrimidine dimer (CPD) accumulation, lower inhibition of cell proliferation, increased cell wall thickness, UV-B absorbing compounds, and ploidy levels, whereas previous data from different groups have shown that CAF-1 mutants show shortening of telomeres, loss of 45S rDNA, and increased homologous recombination, phenotypes associated to DNA breaks. Interestingly, CAF-1 deficient roots show increased inhibition of primary root elongation, with decreased meristem size due to a higher inhibition of cell proliferation after UV-B exposure. The decrease in root meristem size in CAF-1 mutants is a consequence of defects in programmed cell death after UV-B exposure. Together, we provide evidence demonstrating that root and shoot meristematic cells may have distinct protection mechanisms against CPD accumulation by UV-B, which may be linked with different functions of the CAF-1 complex in these different organs.

Different irradiances of UV and PAR in the same ratios alter the flavonoid profiles of Arabidopsis thaliana wild types and UV-signalling pathway mutants

The UVR8 photoreceptor in Arabidopsis thaliana is specific for ultraviolet-B (UV-B; 280-315 nm) radiation and its activation leads to a number of UV-B acclimation responses, including the accumulation of flavonoids. UVR8 participates in a signaling cascade involving COP1 and HY5 so that the absence of any of these components results in a reduction in the ability of a plant to accumulate flavonoids in response to UV; Cop1 mutants show high dropouts and hy5-ks50 hyh double mutants show very low levels of flavonoids. The predominant phenolics in Arabidopsis thaliana are sinapic acid derivatives as well as non-aclyated quercetin and kaempferol di- and triglycosides containing glucose and rhamnose as glycosylated sugar moieties. How this flavonoid profile in Arabidopsis thaliana is affected by UV radiation, how rapidly these changes occur in changing UV conditions, and which components of the UV-B signalling pathway are involved in rapid UV acclimatization reactions is poorly understood. In the present study, we examined these questions by characterizing the flavonoid profiles of Arabidopsis thaliana signalling mutants and wild types grown under different UV levels of constant UV-B+PAR ratios and then transferring a subset of plants to alternate UV conditions. Results indicate that flavonoid accumulation in Arabidopsis thaliana is triggered by UV and this response is amplified by higher levels of UV but not by all compounds to the same extent. The catechol structure in quercetin seems to be less important than the glycosylation pattern, e.g. having 2 rhamnose moieties in determining responsivity. At low UV+PAR intensities the introduction of UV leads to an initial tendency of increase of flavonoids in the wild types that was detected after 3 days. It took 7 days for these changes to be detected in plants grown under high UV+PAR intensities suggesting a priming of PAR. Thus, the flavonoid profile in Arabidopsis thaliana is altered over time following exposure to UV and PAR, but the functional significance of these changes is currently unclear.

UVR8-dependent reporters reveal spatial characteristics of signal spreading in plant tissues

The UV Resistance Locus 8 (UVR8) photoreceptor controls UV-B mediated photomorphogenesis in Arabidopsis. The aim of this work is to collect and characterize different molecular reporters of photomorphogenic UV-B responses. Browsing available transcriptome databases, we identified sets of genes responding specifically to this radiation and are controlled by pathways initiated from the UVR8 photoreceptor. We tested the transcriptional changes of several reporters and found that they are regulated differently in different parts of the plant. Our experimental system led us to conclude that the examined genes are not controlled by light piping of UV-B from the shoot to the root or signalling molecules which may travel between different parts of the plant body but by local UVR8 signalling. The initiation of these universal signalling steps can be the induction of Elongated Hypocotyl 5 (HY5) and its homologue, HYH transcription factors. We found that their transcript and protein accumulation strictly depends on UVR8 and happens in a tissue autonomous manner. Whereas HY5 accumulation correlates well with the UVR8 signal across cell layers, the induction of flavonoids depends on both UVR8 signal and a yet to be identified tissue-dependent or developmental determinant.