DNA DAMAGE AND REPAIR IN PLANTS

Maize lines expressing RNAi to chromatin remodeling factors are similarly hypersensitive to UV-B radiation but exhibit distinct transcriptome responses

RNAi knockdown lines targeting two putative chromatin factors (a methyl-CpG-binding domain protein MBD101 and a chromatin remodeling complex protein CHC101) exhibit identical phenotypic consequences after UV-B exposure including necrosis in adult leaves and seedling death. Here we report that these RNAi lines exhibit substantially different transcriptome changes assessed on a 44 K Agilent oligonucleotide array platform compared to each other and to UV-B tolerant non-transgenic siblings both before and after 8 h of UV-B exposure. Adult maize leaves express approximately 26,000 transcript types under greenhouse growth conditions; after 8 h of UV-B exposure 267 transcripts exhibit an expression change in the B73 control line. Most of these transcript abundance changes in B73 after UV-B treatment are not found in the two RNAi knockdown lines: 119 upregulated transcript types and 128 downregulated types are uniquely modulated in B73. The mbd101 RNAi line shows many more line-specific transcript changes (897 up, 68 down) than either B73 or the chc101 line (72 up, 103 down). By functional analysis, the largest category of genes with predicted functions affected by UV-B is the DNA/chromatin binding group. Differential activation of suites of transcription factors in the control and transgenic lines are the likely explanation for the divergent transcriptome profiles.

Diurnal changes in epidermal UV transmittance of plants in naturally high UV environments

Studies were conducted on three herbaceous plant species growing in naturally high solar UV environments in the subalpine of Mauna Kea, Hawaii, USA, to determine if diurnal changes in epidermal UV transmittance (T(UV)) occur in these species, and to test whether manipulation of the solar radiation regime could alter these diurnal patterns. Additional field studies were conducted at Logan, Utah, USA, to determine if solar UV was causing diurnal T(UV) changes and to evaluate the relationship between diurnal changes in T(UV) and UV-absorbing pigments. Under clear skies, T(UV), as measured with a UV-A-pulse amplitude modulation fluorometer for leaves of Verbascum thapsus and Oenothera stricta growing in native soils and Vicia faba growing in pots, was highest at predawn and sunset and lowest at midday. These patterns in T(UV) closely tracked diurnal changes in solar radiation and were the result of correlated changes in fluorescence induced by UV-A and blue radiation but not photochemical efficiency (F(v)/F(m)) or initial fluorescence yield (F(o)). The magnitude of the midday reduction in T(UV) was greater for young leaves than for older leaves of Verbascum. Imposition of artificial shade eliminated the diurnal changes in T(UV) in Verbascum, but reduction in solar UV had no effect on diurnal T(UV) changes in Vicia. In Vicia, the diurnal changes in T(UV) occurred without detectable changes in the concentration of whole-leaf UV-absorbing compounds. Results suggest that plants actively control diurnal changes in UV shielding, and these changes occur in response to signals other than solar UV; however, the underlying mechanisms responsible for rapid changes in T(UV) remain unclear.

UVB sensitivity and cyclobutane pyrimidine dimer (CPD) photolyase genotypes in cultivated and wild rice species

We investigated the UVB-sensitivity in 12 rice strains belonging to two cultivated species (O. sativa and O. glaberrima) and three wild species (O. barthii, O. meridionalis and O. rufipogon) of rice possessing the AA genome, while focusing on the CPD photolyase activity and the genotypes of CPD photolyase. Although the UVB sensitivity, CPD photolyase activity, and CPD photolyase genotype varied widely among these rice species, the sensitivity to UVB radiation depended on the activity of the CPD photolyase, regardless of grass shape, habitat, or species. The rice strains examined here clearly divided into three groups based on the CPD photolyase activity, and the activity of the strains greatly depended on amino acid residues at positions 126 and 296, with the exception of the W1299 strain (O. meridionalis). The amino acid residues 126 and 296 of CPD photolyase in Sasanishiki strain (O. sativa), which showed higher enzymatic activity and more resistance to UVB, were glutamine (Gln) and Gln, respectively. An amino acid change at position 126 from Gln to arginine ("Nori"-type) in the photolyase led to a reduction of enzymatic activity. Additionally, an amino acid change at position 296 from Gln to histidine led to a further reduction in activity. The activity of the W1299 strain, which possesses a "Nori"-type CPD photolyase, was the highest among the strains examined here, and was similar to that of the Sasanishiki. The CPD photolyase of the W1299 contains ten amino acid substitutions, compared to Sasanishiki. The alterations in amino acid residues in the W1299 CPD photolyase compensated for the reduction in activity caused by the amino acid substitutions at positions 126. Knowledge of the activity of different CPD photolyase genotypes will be useful in developing improved rice cultivars.

Natural UV-Screening Mechanisms of Norway Spruce (Picea abies [L.] Karst.) Needles

Ultraviolet-light screening potential of Norway spruce (Picea abies [L.] Karst.) needles was investigated by UV-spectroscopic, microscopic, fluorescence spectroscopic techniques as well as by HPLC, mass spectrometry and NMR spectroscopy. Results showed four potential barriers of UV screening by Norway spruce needles: (1) UV-light screening via reflectance of UV/violet light by epidermis, (2) UV-light screening via reduction of transmission of UV light by special anatomical arrangement of the epidermal cells containing the UV-screening allomelanins as well as by the light-reflecting hyaline hypodermal cells, (3) conversion of UV light by epidermis into photosynthetically active radiation (PAR; blue and red spectral bands) via fluorescence and (4) UV-light screening by absorption of UV light by UV-screening substances contained in the epidermis, whereby the latter was found to be the most important UV-screening mechanism. Staining of needle cross sections with Naturstoffreagenz A showed the localization of bound flavonoids and its derivatives in the cell walls of the outer epidermal cell layer as revealed by confocal laser scanning microscopy. By fluorescence spectroscopy and confocal laser scanning microscopy, the conversion of UVA light into PAR in the epidermis was related to various UV-screening substances contained in the epidermis. The methanol-soluble UV-absorbing substances were found to create novel UV-screening barrier zones: UVC, >200-253 nm; UVC/UVB, >253-300/303 nm; and UVB/UVA, >300-362/368 nm in epidermis as well as in mesophyll (±vascular bundles) tissues, suggesting the protective functions of epidermis for the underlying mesophyll as well as of mesophyll for the underlying vascular bundles. The following sequence of efficiency of UV-screening barrier zones of the methanol-soluble extracts of the needle epidermis and mesophyll (± vascular bundles) for various UV-spectral bands was detected: UVC screening at less than 265 nm > UVC screening at 265-280 nm > UVB screening at 280–320 nm > UVA screening at 320–400 nm, whereby the UV screening at 280-320 nm was suggested as the most relevant barrier against enhanced UVB radiation. A blend of various UV-screening substances occurred in the methanol-soluble fractions of needle epidermis, whereby p-hydroxybenzoic acid 4-O-β-D-glucopyranoside, picein, (+)-catechin, p-hydroxyacetophenone, benzoic acid and astragalin were identified as UVC/UVB-screening substances; picein, (+)-catechin, astringin, p-hydroxyacetophenone and astragalin(s) as UVB-screening substances and astragalin(s) as UVA/B-screening substances. Alkaline hydrolysis of methanol-insoluble epidermal cell wall fractions released p-coumaric acid, ferulic acid and as-tragalin(s) as major UVB-screening substances. Loss of vitality of Norway spruce trees (forest decline disease) led to a significant reduction of UVB (315 nm)-screening ability of methanol-soluble fractions from epidermis, mesophyll (±vascular bundles) and whole needles. The HPLC analysis showed that the loss of vitality is due to a reduction in accumulation of UVB-absorbing substances, mainly picein, (+)-catechin, isorhapontin and astragalin(s) in the epidermis of needles from the second needle year in accordance with the detected loss of UVB-screening ability. It is concluded that the natural UV-screening mechanisms of Norway spruce needles are highly complex but mainly actively mediated by the ability of methanol-soluble UV-absorbing substances to form variable UVB-AJVA-screening barrier zones and passively by the ability of epidermal cell wall-bound UV-screening substances to screen UV light, whereby in the epidermis a conversion of excess UV light into PAR takes place.

Continuous UV-B irradiation induces morphological changes and the accumulation of polyphenolic compounds on the surface of cucumber cotyledons

Sharp-headed and globular-headed trichomes are found on the surface of cucumber (Cucumis sativus L.) cotyledons. Most sharp-headed trichomes consist of three cells. Toluidine blue O stains sharp-headed but not globular-headed trichomes. The effect of continuous ultraviolet-B (UV-B; 290-320 nm) irradiation on the surface of cucumber cotyledons was examined with respect to the two trichome types. Continuous UV-B irradiation induced cell division at or under the basal part of sharp-headed trichomes, resulting in an increase in the number of cell layers from three to six. In parallel, the area stained by toluidine blue O expanded to include epidermal cells surrounding sharp-headed trichomes. Regions of alkali-induced fluorescence due to the presence of polyphenolic compounds coincided with areas stained by toluidine blue O. In contrast, continuous UV-B irradiation did not cause morphological changes in globular-headed trichomes. Thus, continuous UV-B irradiation causes the accumulation of polyphenolic compounds in cucumber cotyledons and induces specific morphological changes in or around sharp-headed trichomes. UV-B exposure also increases lignin content in this tissue. Therefore, continuous UV-B irradiation may induce the specific accumulation of polyphenolic compounds, especially stress lignins, in and near sharp-headed trichomes.

Proteomics-based dissection of stress-responsive pathways in plants

Abiotic stress has an ability to alter the levels of a number of proteins, which may be soluble or structural in nature or which may exist before and after folding in the plant cell. The most crucial function of plant cell is to respond to stress by developing defence mechanisms. This defence is brought about by alteration in the pattern of gene expression. This leads to modulation of certain metabolic and defensive pathways. Owing to gene expression altered under stress, qualitative and quantitative changes in proteins are obvious. These proteins might play a role in signal transduction, antioxidative defence, antifreezing, heat shock, metal binding, antipathogenesis or osmolyte synthesis. A significant part of the literature shows the quantitative and qualitative changes in proteins, mainly employing western analysis, enzymatic kinetics, fraction isolation, one-dimensional SDS-PAGE electrophoresis, etc. Fortunately, recent developments in sensitivity and accuracy for proteome analysis have provided new dimensions to assess the changes in protein types and their expression levels under stress. The novel aim of this review is to do a side-by-side comparison of the proteins that are induced or overexpressed under abiotic stress, examining those from biochemical literature and the ones observed, sequenced and identified using the advanced proteomics and bioinformatic techniques.

Induction and inhibition of cyclobutane pyrimidine dimer photolyase in etiolated cucumber (Cucumis sativus) cotyledons after ultraviolet irradiation depends on wavelength

Under polychromatic ultraviolet (UV) irradiation (maximum energy at 327 nm) the activity of DNA photolyase specific to cyclobutane pyrimidine dimers (CPDs), CPD photolyase, increased by an amount which depended on UV irradiance, and the level of CPD photolyase gene (CsPHR) transcripts temporarily increased before the activity reached a constant level. UV light (>320 nm) was more effective than visible light at increasing CPD photolyase activity. In contrast, monochromatic UV irradiation at wavelengths <300 nm increased the level of CsPHR transcripts similarly to irradiation at wavelengths >320 nm, but reduced CPD photolyase activity compared with the dark control. Exposure of a CPD photolyase solution to UV-C (254 nm) reduced enzyme activity and induced accumulation of H(2)O(2). Addition of H(2)O(2) to the enzyme solution also inactivated CPD photolyase activity. These results suggest the possibility that reactive oxygen species participate in the inactivation of CPD photolyase in cotyledons exposed to UV irradiation of <300 nm.

Increase in CPD photolyase activity functions effectively to prevent growth inhibition caused by UVB radiation

Rice cultivars vary widely in their sensitivity to ultraviolet B (UVB) and this has been correlated with cyclobutane pyrimidine dimer (CPD) photolyase mutations that alter the structure/function of this photorepair enzyme. Here, we tested whether CPD photolyase function determines the UVB sensitivity of rice (Oryza sativa) by generating transgenic rice plants bearing the CPD photolyase gene of the UV-resistant rice cultivar Sasanishiki in the sense orientation (S-B and S-C lines) or the antisense orientation (AS-D line). The S-B and S-C plants had 5.1- and 45.7-fold higher CPD photolyase activities than the wild-type, respectively, were significantly more resistant to UVB-induced growth damage, and maintained significantly lower CPD levels in their leaves during growth under elevated UVB radiation. Conversely, the AS-D plant had little photolyase activity, was severely damaged by elevated UVB radiation, and maintained higher CPD levels in its leaves during growth under UVB radiation. Notably, the S-C plant was not more resistant to UVB-induced growth inhibition than the S-B plant, even though it had much higher CPD photolyase activity. These results strongly indicate that UVB-induced CPDs are one of principal causes of UVB-induced growth inhibition in rice plants grown under supplementary UVB radiation, and that increasing CPD photolyase activity can significantly alleviate UVB-caused growth inhibition in rice. However, further protection from UVB-induced damage may require the genetic enhancement of other systems as well.

The effects of ultraviolet radiation on photosynthetic performance, growth and sunscreen compounds in aeroterrestrial biofilm algae isolated from building facades

The effects of artificial ultraviolet radiation [UVR; 8 W m(-2) ultraviolet-A (UVA), 0.4 W m(-2) ultraviolet-B (UVB)] on photosynthetic performance, growth and the capability to synthesise mycosporine-like amino acids (MAAs) was investigated in the aeroterrestrial green algae Stichococcus sp. and Chlorella luteoviridis forming biofilms on building facades, and compared with the responses of two green algae, from soil (Myrmecia incisa) and brackish water (Desmodesmus subspicatus). All species exhibited decreasing quantum efficiency (Fv/Fm) after 1-3 days exposure to UVR. After 8-12 days treatment, however, all aeroterrestrial isolates exhibited full recovery under UVA and UVA/B. In contrast, D. subspicatus showed only 80% recovery after treatment with UVB. While Stichococcus sp. and C. luteoviridis exhibited a broad tolerance in growth under all radiation conditions tested, M. incisa showed a significant decrease in growth rate after exposure to UVA and UVA/B. Similarly D. subspicatus grew with a reduced rate under UVA, but UVA/B led to full inhibition. Using HPLC, an UV-absorbing MAA (324 nm-MAA) was identified in Stichococcus sp. and C. luteoviridis. While M. incisa contained a specific 322 nm-MAA, D. subspicatus lacked any trace of such compounds. UV-exposure experiments indicated that all MAA-containing species are capable of synthesizing and accumulating these compounds, thus supporting their function as an UV-sunscreen. All data well explain the conspicuous ecological success of aeroterrestrial green algae in biofilms on facades. Biosynthesis and accumulation of MAAs under UVR seem to result in a reduced UV-sensitivity of growth and photosynthesis, which consequently may enhance survival in the environmentally harsh habitat.

Environmental and developmental effects on the biosynthesis of UV-B screening pigments in Scots pine (Pinus sylvestris L.) needles

The major UV-B screening pigments of the epidermal layer of Scots pine (Pinus sylvestris) needles are flavonol 3-o-glycosides (F3Gs) esterified with hydroxycinnamic acids at positions 3" and 6". Acylation is the last step in biosynthesis and is catalysed by position-specific hydroxycinnamoyl transferases (3" and 6"HCT). The UV-B dependence of these enzyme activities was studied in primary needles of Scots pine seedlings grown under different UV-B conditions in environmentally controlled sun simulators. 6"HCT activity was induced upon UV-B irradiation while 3"HCT activity was not induced but showed high constitutive values. To investigate the biosynthesis of diacylated F3Gs during needle development under natural conditions, the HCT activities and metabolite contents were analysed in needles of field-grown mature pine trees. Accumulation of diacylated compounds as well as of 6"HCT activity occurred transiently in the first year of needle development only. In contrast, 3"HCT activity exhibited broad maxima in two consecutive years during needle growth. The data suggest that acylated F3Gs are first formed as soluble compounds which are then translocated into the cell wall to be bound by their hydroxycinnamoyl residues.

Sensitivity of rice to ultraviolet-B radiation

BACKGROUND

Depletion of the stratospheric ozone layer leads to an increase in ultraviolet-B (UVB: 280-320 nm) radiation reaching the earth's surface, and the enhanced solar UVB radiation predicted by atmospheric models will result in reduction of growth and yield of crops in the future. Over the last two decades, extensive studies of the physiological, biochemical and morphological effects of UVB in plants, as well as the mechanisms of UVB resistance, have been carried out.

SCOPE

In this review, we describe recent research into the mechanisms of UVB resistance in higher plants, with an emphasis on rice (Oryza sativa), one of the world's most important staple food crops. Recent studies have brought to light the following remarkable findings. UV-absorbing compounds accumulating in the epidermal cell layers have traditionally been considered to function as UV filters, and to play an important role in countering the damaging effects of UVB radiation. Although these compounds are effective in reducing cyclobutane pyrimidine dimer (CPD) induction in plants exposed to a challenge exposure to UVB, certain levels of CPD are maintained constitutively in light conditions containing UVB, regardless of the quantity or presence of visible light. These findings imply that the systems for repairing DNA damage and scavenging reactive oxygen species (ROS) are essential for plants to grow in light conditions containing UVB.

CONCLUSION

CPD photolyase activity is a crucial factor determining the differences in UVB sensitivity between rice cultivars. The substitution of one or two bases in the CPD photolyase gene can alter the activity of the enzyme, and the associated resistance of the plant to UVB radiation. These findings open up the possibility, in the near future, of increasing the resistance of rice to UVB radiation, by selective breeding or bioengineering of the genes encoding CPD photolyase.

Characterization of T-DNA insertion mutants and RNAi silenced plants of Arabidopsis thaliana UV-damaged DNA binding protein 2 (AtUV-DDB2)

The human UV-damaged DNA binding protein (UV-DDB), a heterodimeric protein composed of 127 kDa (UV-DDB1) and 48 kDa (UV-DDB2) subunits, has been shown to be involved in DNA repair. To elucidate the in vivo function of plant UV-DDB2, we have analyzed T-DNA insertion mutants of the Arabidopsis thaliana UV-DDB2 subunit (atuv-ddb2 mutants) and AtUV-DDB2 RNAi silenced plants (atuv-ddb2 silenced plants). atuv-ddb2 mutants and atuv-ddb2 silenced plants were both viable, suggesting that AtUV-DDB2 is not essential for survival. Interestingly, both plant types showed a dwarf phenotype, implying impaired growth of the meristem. To the best of our knowledge, this is the first occasion that a dwarf phenotype has been found to be associated with a UV-DDB2 mutation in either plants or animals. The mutants also demonstrated increased sensitivity to UV irradiation, methyl methanesulfonate and hydrogen peroxide treatment, indicating that AtUV-DDB2 is also involved in DNA repair. Our results lead us to suggest that not only does AtUV-DDB2 function in DNA repair, it also has a direct or indirect influence on cell proliferation in the plant meristem.

Arabidopsis homologue of human transcription factor IIH/nucleotide excision repair factor p44 can function in transcription and DNA repair and interacts with AtXPD

Eukaryotic general transcription factor (TF) IIH is composed of 10 proteins, seven of which are also required for nucleotide excision repair (NER) of UV radiation-induced DNA damage in human cells and yeast. Plant homologues of the human TFIIH subunits XPB and XPD that function in NER have been isolated but none has been shown to operate in transcription. Here we address the capabilities of Arabidopsis thaliana AtGTF2H2 and AtXPD, homologues of the essential interacting human/yeast TFIIH components p44/Ssl1 and XPD/Rad3, respectively. Expression of AtGTF2H2 or AtXPD cDNAs in yeast ssl1 or rad3 mutants temperature-sensitive for growth due to thermolabile transcription of mRNA restored growth and so transcription at the non-permissive temperature. AtGTF2H2 also complemented the NER deficiency of the corresponding yeast mutant, as measured by full recovery of UV resistance, whereas AtXPD did not despite being necessary for NER in Arabidopsis. UV treatment did not upregulate transcription of AtGTF2H2 or AtXPD in Arabidopsis. Suppression of a yeast translation initiation defect by the ssl1-1 mutation was prevented by expression of AtGTF2H2. Deletion of SSL1 in a yeast strain expressing AtGTF2H2 did not affect growth or confer UV sensitivity, demonstrating that AtGTF2H2 can perform all essential transcription functions and UV damage repair duties of Ssl1 in its absence. Furthermore, AtGTF2H2 interacted with AtXPD and yeast Rad3, and AtXPD also interacted with yeast Ssl1 in two-hybrid assays. Our results indicate that AtGTF2H2 can act in transcription and NER, and suggest that it participates in both processes in Arabidopsis as part of TFIIH.

Oxidative DNA damage in cucumber cotyledons irradiated with ultraviolet light

DNA was isolated from the cotyledons of cucumber seedlings irradiated with ultraviolet (UV)-C (254 nm) or UV-B+UV-A (280-360 nm; maximum energy at 312 nm) at various fluence rates and durations. Following enzymatic hydrolysis of DNA, the content of 8-hydroxy-2'-deoxyguanosine [(8-OHdG), 8-oxo-7,8-dihydro-2'-deoxyguanosine], a well-established biomarker closely identified with carcinogenesis and aging in animal cells, was determined using a high-performance liquid chromatograph equipped with an electrochemical detector. The levels of 8-OHdG increased with UV-C and UV-B irradiation in a fluence-dependent manner. This increase was also observed in etiolated cotyledons that had been excised from dark-grown cucumber seedlings and then cultured in vitro under UV light: monochromatic UV light at 270 nm or 290 nm increased the 8-OHdG level considerably, while UV at wavelengths above 310 nm had only small effects. In situ detection of H2O2 and quantification of H2O2 in plant extracts revealed that H2O2 accumulated in cotyledons irradiated with UV light. These results suggest that UV irradiation induces oxidative DNA damage in plant cells.

Nocturnal changes in leaf growth of Populus deltoides are controlled by cytoplasmic growth

Growing leaves do not expand at a constant rate but exhibit pronounced diel growth rhythms. However, the mechanisms giving rise to distinct diel growth dynamics in different species are still largely unknown. As a first step towards identifying genes controlling rate and timing of leaf growth, we analysed the transcriptomes of rapidly expanding and fully expanded leaves of Populus deltoides Bartr. ex. Marsh at points of high and low expansion at night. Tissues with well defined temporal growth rates were harvested using an online growth-monitoring system based on a digital image sequence processing method developed for quantitative mapping of dicot leaf growth. Unlike plants studied previously, leaf growth in P. deltoides was characterised by lack of a base-tip gradient across the lamina, and by maximal and minimal growth at dusk and dawn, respectively. Microarray analysis revealed that the nocturnal decline in growth coincided with a concerted down-regulation of ribosomal protein genes, indicating deceleration of cytoplasmic growth. In a subsequent time-course experiment, Northern blotting and real-time RT-PCR confirmed that the ribosomal protein gene RPL12 and a cell-cycle gene H2B were down-regulated after midnight following a decrease in cellular carbohydrate concentrations. Thus, we propose that the spatio-temporal growth pattern in leaves of P. deltoides primarily arises from cytoplasmic growth whose activity increases from afternoon to midnight and thereafter decreases in this species.

Homologous recombination in plants is organ specific

In this paper we analysed the genome stability of various Arabidopsis thaliana plant organs using a transgenic recombination system. The system was based on two copies of non-functional GUS (lines #651 and #11) or LUC (line #15D8) reporter genes serving as a recombination substrate. Both reporter assays showed that recombination in flowers or stems were rare events. Most of the recombination sectors were found in leaves and roots, with leaves having over 2-fold greater number of the recombination events per single cell genome as compared to roots. The recombination events per single genome were 9.7-fold more frequent on the lateral half of the leaves than on the medial halves. This correlated with a 2.5-fold higher metabolic activity in the energy source (lateral) versus energy sink (medial) of leaves. Higher metabolic activity was paralleled by a higher anthocyanin production in lateral halves. The level of double strand break (DSB) occurrence was also different among plant organs; the highest level was observed in roots and the lowest in leaves. High level of DSBs strongly positively correlated with the activity of the key repair enzymes, AtKU70 and AtRAD51. The ratio of AtRAD51 to AtKU70 expression was the highest in leaves, supporting the more active involvement of homologous recombination pathway in the repair of DSBs in this organ. Western blot analysis confirmed the real time PCR expression data for AtKU70 gene.

Characterization of the three Arabidopsis thaliana RAD21 cohesins reveals differential responses to ionizing radiation

The RAD21/REC8 gene family has been implicated in sister chromatid cohesion and DNA repair in several organisms. Unlike most eukaryotes, Arabidopsis thaliana has three RAD21 gene homologues, and their cloning and characterization are reported here. All three genes, AtRAD21.1, AtRAD21.2, and AtRAD21.3, are expressed in tissues rich in cells undergoing cell division, and AtRAD21.3 shows the highest relative level of expression. An increase in steady-state levels of AtRAD21.1 transcript was also observed, specifically after the induction of DNA damage. Phenotypic analysis of the atrad21.1 and atrad21.3 mutants revealed that neither of the single mutants was lethal, probably due to the redundancy in function of the AtRAD21 genes. However, AtRAD21.1 plays a critical role in recovery from DNA damage during seed imbibition, prior to germination, as atrad21.1 mutant seeds are hypersensitive to radiation damage.

Plant responses to UV radiation and links to pathogen resistance

Increased incident ultraviolet (UV) radiation due to ozone depletion has heightened interest in plant responses to UV because solar UV wavelengths can reduce plant genome stability, growth, and productivity. These detrimental effects result from damage to cell components including nucleic acids, proteins, and membrane lipids. As obligate phototrophs, plants must counter the onslaught of cellular damage due to prolonged exposure to sunlight. They do so by attenuating the UV dose received through accumulation of UV-absorbing secondary metabolites, neutralizing reactive oxygen species produced by UV, monomerizing UV-induced pyrimidine dimers by photoreactivation, extracting UV photoproducts from DNA via nucleotide excision repair, and perhaps transiently tolerating the presence of DNA lesions via replicative bypass of the damage. The signaling mechanisms controlling these responses suggest that UV exposure also may be beneficial to plants by increasing cellular immunity to pathogens. Indeed, pathogen resistance can be enhanced by UV treatment, and recent experiments suggest DNA damage and its processing may have a role.

On the role of flavonoids in the integrated mechanisms of response of Ligustrum vulgare and Phillyrea latifolia to high solar radiation

The role of flavonoids in mechanisms of acclimation to high solar radiation was analysed in Ligustrum vulgare and Phillyrea latifolia, two Mediterranean shrubs that have the same flavonoid composition but differ strikingly in their leaf morpho-anatomical traits. In plants exposed to 12 or 100% solar radiation, measurements were made for surface morphology and leaf anatomy; optical properties, photosynthetic pigments, and photosystem II efficiency; antioxidant enzymes, lipid peroxidation and phenylalanine ammonia lyase; synthesis of hydroxycinnamates and flavonoids; and the tissue-specific distribution of flavonoid aglycones and ortho-dihydroxylated B-ring flavonoid glycosides. A denser indumentum of glandular trichomes, coupled with both a thicker cuticle and a larger amount of cuticular flavonoids, allowed P. latifolia to prevent highly damaging solar wavelengths from reaching sensitive targets to a greater degree than L. vulgare. Antioxidant enzymes in P. latifolia were also more effective in countering light-induced oxidative load than those in L. vulgare. Consistently, light-induced accumulation of flavonoids in L. vulgare, particularly ortho-dihydroxylated flavonoids in the leaf mesophyll, greatly exceeded that in P. latifolia. We conclude that the accumulation of flavonoid glycosides associated with high solar radiation-induced oxidative stress and, hence, biosynthesis of flavonoids appear to be unrelated to 'tolerance' to high solar radiation in the species examined.

Analysis of leaf proteome after UV-B irradiation in maize lines differing in sensitivity

UV-B radiation causes diverse morphological and physiological responses in plants, but the underlying mechanisms governing these integrated responses are unknown. In this study, we systematically surveyed responses of maize leaves to UV-B radiation using DIGE 2D gels and identified selected proteins by mass spectrometry and immunodetection analysis. To identify changes in protein accumulation in response to UV-B radiation, a line (b, pl W23) deficient in flavonoid sunscreen compounds and hence similar to commercial corn was used. In addition, its proteome in natural UV-B conditions was compared with that of two maize landraces from high altitudes (Cacahuacintle and Confite Puneño) that have improved UV-B tolerance. Protein patterns in adult maize leaves (Zea mays) were documented after growth for 21 days in sunlight depleted of UV-B radiation or growth in sunlight including an 8-h UV-B supplementation during 1 day in the field. We found that there is a very high correlation between previously documented mRNA accumulation assessed by microarray hybridization and quantitative real time reverse transcription-PCR and protein expression after UV-B irradiation in leaves of W23. Multiple isoforms were confirmed for some proteins; at least one protein, pyruvate, phosphate dikinase, is regulated post-translationally by phosphorylation by UV-B exposure. Proteins differentially regulated by UV-B radiation in W23 with higher levels under similar UV-B conditions in high altitude plants were also identified. These could be genetically fixed traits conferring UV-B tolerance and offer clues to specific adaptations to living in high ambient UV-B conditions.

Genomic mutation in lines of Arabidopsis thaliana exposed to ultraviolet-B radiation

Studies that have attempted to estimate the rate of deleterious mutation have typically been conducted under low levels of ultraviolet-B (UV-B) radiation, a naturally occurring mutagen. We conducted experiments to test whether the inclusion of natural levels of UV-B radiation in mutation-accumulation (MA) experiments influences the rate and effects of mildly deleterious mutation in the plant Arabidopsis thaliana. Ten generations of MA proved insufficient to observe significant changes in means or among-line variances in experimental lines maintained either with or without supplemental UV-B radiation. Maximum-likelihood estimates of mutation rate for total flower number revealed a small but significant rate of mutation for MA lines propagated under supplemental UV-B exposure, but not for those in which supplemental UV-B was omitted. A fraction of the flower number mutations under UV-B (approximately 25-30%) are estimated to increase flower number. Results from the application of transposon display to plant materials obtained after MA, in both the presence and absence of supplemental UV-B, suggest that the average rate of transposition for the class I and II transposable elements (TEs) surveyed was no more than 10(-4). Overall, the estimates of mutation parameters are qualitatively similar to what has been observed in other MA experiments with this species in which supplemental UV-B levels have not been used. As well, it appears that naturally occurring levels of UV-B do not lead to detectable increases in levels of transposable element activity.

Spontaneously occurring mutations in the cyclobutane pyrimidine dimer photolyase gene cause different sensitivities to ultraviolet-B in rice

Sensitivity to ultraviolet-B (UVB) radiation (280-320 nm) varies widely among rice cultivars. We previously indicated that UV-resistant rice cultivars are better able to repair cyclobutane pyrimidine dimers (CPDs) through photorepair than are UV-sensitive cultivars. In this paper, we report that UVB sensitivity in rice, in part, is the result of defective CPD photolyase alleles. Surjamkhi (indica) exhibited greater sensitivity to UVB radiation and was more deficient in CPD photorepair ability compared with UV-resistant Sasanishiki (japonica). The deficiency in CPD photorepair in Surjamkhi resulted from changes in two nucleotides at positions 377 and 888 in the photolyase gene, causing alterations of two deduced amino acids at positions 126 and 296 in the photolyase enzyme. A linkage analysis in populations derived from Surjamkhi and Sasanishiki showed that UVB sensitivity is a quantitative inherited trait and that the CPD photolyase locus is tightly linked with a quantitative trait locus that explains a major portion of the genetic variation for this trait. These results suggest that spontaneously occurring mutations in the CPD photolyase gene cause different degrees of sensitivity to UVB in rice, and that the resistance of rice to UVB radiation could be increased by increasing the photolyase function through conventional breeding or bioengineering.

Is UV-B radiation affecting charophycean algae in shallow freshwater systems?

The objective of this study was to determine the effects of UV-B radiation on charophycean algae under natural conditions, since charophytes enhance water transparency in freshwater systems and levels of UV-B radiation have increased by ozone depletion. Potential and actual UV-B effects were studied by combining a glasshouse experiment in which plants were exposed to various levels of UV-B radiation and field measurements in two freshwater systems dominated by charophytes in the Netherlands. The glasshouse experiment showed that charophytes were sensitive to UV-B radiation. UV-B radiation negatively affected growth, while it increased levels of DNA damage in Chara aspera. Moreover, the charophytes did not seem to develop UV-B screens to protect against UV-B radiation since no increase in UV-B absorbing compounds was found. At field conditions, both spectroradiometrical measurements and DNA dosimeters showed that UV-B radiation was attenuated quickly in both freshwater systems, indicating that UV-B does not reach the submerged charophyte vegetation. However, specific conditions, like fluctuating water tables, may result in UV-B exposure to charophytes for certain periods annually.

Homologous recombination in plants is temperature and day-length dependent

Homologous recombination (HR) as a strand break repair mechanism was shown to be influenced by various factors. The balance of different vitamins, macro- and microelements, light spectrum, sodium chloride concentration as well as various environmental mutagens were shown to influence the frequency of HR. In this paper we analysed the influence of temperature (4, 22, and 32 degrees C) and day/night duration on the genome stability of plants. We analyzed the HR frequency in transgenic Arabidopsis thaliana plants carrying beta-glucuronidase based homologous recombination substrate. To find the recombination rate (RR), we related the HR frequency to the number of genomes present in plants grown under different conditions. The RR was also standardized to the transcription activity of the transgene. We found RR to be higher in plants grown at suboptimal temperatures (either 4 or 32 degrees C) as compared to plants grown at 22 degrees C. This negatively correlated with the plant metabolic rate and positively correlated with concentration of peroxide produced by plant. In contrast, the RR in plants grown at different day length (8-24 h) was the lowest in plants grown at the longest day (24 h) and highest in the plants grown at the shortest day (8 h). Over 15-fold difference in the RR between plants grown at the shortest and the longest day was observed. Such a difference in recombination rate was primarily due to the higher transgene activity and higher endoreduplication levels in plants grown at longer days. Our data suggests that even "moderate" changes of environmental conditions may have a significant effect on plant genome stability.

Arabidopsis DNA double-strand break repair pathways

DSBs (double-strand breaks) are one of the most serious forms of DNA damage that can occur in a cell's genome. DNA replication in cells containing DSBs, or following incorrect repair, may result in the loss of large amounts of genetic material, aneuploid daughter cells and cell death. There are two major pathways for DSB repair: HR (homologous recombination) uses an intact copy of the damaged region as a template for repair, whereas NHEJ (non-homologous end-joining) rejoins DNA ends independently of DNA sequence. In most plants, NHEJ is the predominant DSB repair pathway. Previously, the Arabidopsis NHEJ mutant atku80 was isolated and found to display hypersensitivity to bleomycin, a drug that causes DSBs in DNA. In the present study, the transcript profiles of wild-type and atku80 mutant plants grown in the presence and absence of bleomycin are determined by microarray analysis. Several genes displayed very strong transcriptional induction specifically in response to DNA damage, including the characterized DSB repair genes AtRAD51 and AtBRCA1. These results identify novel candidate genes that encode components of the DSB repair pathways active in NHEJ mutant plants.

Components of nucleotide excision repair and DNA damage tolerance in Arabidopsis thaliana

As obligate phototrophs, and despite shielding strategies, plants sustain DNA damage caused by UV radiation in sunlight. By inhibiting DNA replication and transcription, such damage may contribute to the detrimental effects of UV radiation on the growth, productivity, and genetic stability of higher plants. However, there is evidence that plants can reverse UV-induced DNA damage by photoreactivation or remove it via nucleotide excision repair. In addition, plants may have mechanisms for tolerating UV photoproducts as a means of avoiding replicative arrest. Recently, phenotypic characterization of plant mutants, functional complementation studies, and cDNA analysis have implicated genes isolated from the model plant Arabidopsis thaliana in nucleotide excision repair or tolerance of UV-induced DNA damage. Here, we briefly review features of these processes in human cells, collate information on Arabidopsis homologs of the relevant genes, and summarize the experimental findings that link certain of these plant genes to nucleotide excision repair or damage tolerance.

Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function

BACKGROUND

The analysis of synonymous and nonsynonymous rates of DNA change can help in the choice among competing explanations for rate variation, such as differences in constraint, mutation rate, or the strength of genetic drift. Nonphotosynthetic plants of the Orobanchaceae have increased rates of DNA change. In this study 38 taxa of Orobanchaceae and relatives were used and 3 plastid genes were sequenced for each taxon.

RESULTS

Phylogenetic reconstructions of relative rates of sequence evolution for three plastid genes (rbcL, matK and rps2) show significant rate heterogeneity among lineages and among genes. Many of the non-photosynthetic plants have increases in both synonymous and nonsynonymous rates, indicating that both (1) selection is relaxed, and (2) there has been a change in the rate at which mutations are entering the population in these species. However, rate increases are not always immediate upon loss of photosynthesis. Overall there is a poor correlation of synonymous and nonsynonymous rates. There is, however, a strong correlation of synonymous rates across the 3 genes studied and the lineage-speccific pattern for each gene is strikingly similar. This indicates that the causes of synonymous rate variation are affecting the whole plastid genome in a similar way. There is a weaker correlation across genes for nonsynonymous rates. Here the picture is more complex, as could be expected if there are many causes of variation, differing from taxon to taxon and gene to gene.

CONCLUSIONS

The distinctive pattern of rate increases in Orobanchaceae has at least two causes. It is clear that there is a relaxation of constraint in many (though not all) non-photosynthetic lineages. However, there is also some force affecting synonymous sites as well. At this point, it is not possible to tell whether it is generation time, speciation rate, mutation rate, DNA repair efficiency or some combination of these factors.

Ultraviolet-B sensitivities in Japanese lowland rice cultivars: cyclobutane pyrimidine dimer photolyase activity and gene mutation

There is a cultivar difference in the response to ultraviolet-B (UVB: 280-320 nm) in rice (Oryza sativa L.). Among Japanese lowland rice cultivars, Sasanishiki, a leading Japanese rice cultivar, is resistant to the damaging effects of UVB while Norin 1, a close relative, is less resistant. We found previously that Norin 1 was deficient in cyclobutane pyrimidine dimer (CPD) photorepair ability and suggested that the UVB sensitivity in rice depends largely on CPD photorepair ability. In order to verify that suggestion, we examined the correlation between UVB sensitivity and CPD photolyase activity in 17 rice cultivars of progenitors and relatives in breeding of UV-resistant Sasanishiki and UV-sensitive Norin 1. The amino acid at position 126 of the deduced amino acid sequence of CPD photolyase in cultivars including such as Norin 1 was found to be arginine, the CPD photolyase activities of which were lower. The amino acid at that position in cultivars including such as Sasanishiki was glutamine. Furthermore, cultivars more resistant to UVB were found to exhibit higher photolyase activities than less resistant cultivars. These results emphasize that single amino acid alteration from glutamine to arginine leads to a deficit of CPD photolyase activity and that CPD photolyase activity is one of the main factors determining UVB sensitivity in rice.

Functional XPB/RAD25 redundancy in Arabidopsis genome: characterization of AtXPB2 and expression analysis

The xeroderma pigmentosum complementation group B (XPB) protein is involved in both DNA repair and transcription in human cells. It is a component of the transcription factor IIH (TFIIH) and is responsible for DNA helicase activity during nucleotide (nt) excision repair (NER). Its high evolutionary conservation has allowed identification of homologous proteins in different organisms, including plants. In contrast to other organisms, Arabidopsis thaliana harbors a duplication of the XPB orthologue (AtXPB1 and AtXPB2), and the proteins encoded by the duplicated genes are very similar (95% amino acid identity). Complementation assays in yeast rad25 mutant strains suggest the involvement of AtXPB2 in DNA repair, as already shown for AtXPB1, indicating that these proteins may be functionally redundant in the removal of DNA lesions in A. thaliana. Although both genes are expressed in a constitutive manner during the plant life cycle, Northern blot analyses suggest that light modulates the expression level of both XPB copies, and transcript levels increase during early stages of development. Considering the high similarity between AtXPB1 and AtXPB2 and that both of predicted proteins may act in DNA repair, it is possible that this duplication may confer more flexibility and resistance to DNA damaging agents in thale cress.

Crosslinking of ribosomal proteins to RNA in maize ribosomes by UV-B and its effects on translation

Ultraviolet-B (UV-B) photons can cause substantial cellular damage in biomolecules, as is well established for DNA. Because RNA has the same absorption spectrum for UV as DNA, we have investigated damage to this cellular constituent. In maize (Zea mays) leaves, UV-B radiation damages ribosomes by crosslinking cytosolic ribosomal proteins S14, L23a, and L32, and chloroplast ribosomal protein L29 to RNA. Ribosomal damage accumulated during a day of UV-B exposure correlated with a progressive decrease in new protein production; however, de novo synthesis of some ribosomal proteins is increased after 6 h of UV-B exposure. After 16 h without UV-B, damaged ribosomes were eliminated and translation was restored to normal levels. Ribosomal protein S6 and an S6 kinase are phosphorylated during UV-B exposure; these modifications are associated with selective translation of some ribosomal proteins after ribosome damage in mammalian fibroblast cells and may be an adaptation in maize. Neither photosynthesis nor pigment levels were affected significantly by UV-B, demonstrating that the treatment applied is not lethal and that maize leaf physiology readily recovers.

Unintended effects and their detection in genetically modified crops

The commercialisation of GM crops in Europe is practically non-existent at the present time. The European Commission has instigated changes to the regulatory process to address the concerns of consumers and member states and to pave the way for removing the current moratorium. With regard to the safety of GM crops and products, the current risk assessment process pays particular attention to potential adverse effects on human and animal health and the environment. This document deals with the concept of unintended effects in GM crops and products, i.e. effects that go beyond that of the original modification and that might impact primarily on health. The document first deals with the potential for unintended effects caused by the processes of transgene insertion (DNA rearrangements) and makes comparisons with genetic recombination events and DNA rearrangements in traditional breeding. The document then focuses on the potential value of evolving "profiling" or "omics" technologies as non-targeted, unbiased approaches, to detect unintended effects. These technologies include metabolomics (parallel analysis of a range of primary and secondary metabolites), proteomics (analysis of polypeptide complement) and transcriptomics (parallel analysis of gene expression). The technologies are described, together with their current limitations. Importantly, the significance of unintended effects on consumer health are discussed and conclusions and recommendations presented on the various approaches outlined.

Rapid transcriptome responses of maize (Zea mays) to UV-B in irradiated and shielded tissues

Profiling the transcriptional response of maize tissues to UV-B irradiation suggests that a signal is transmitted from irradiated to shielded tissue. The transcriptional response occurs rapidly, even in shielded tissue.

Background

Depletion of stratospheric ozone has raised terrestrial levels of ultraviolet-B radiation (UV-B), an environmental change linked to an increased risk of skin cancer and with potentially deleterious consequences for plants. To better understand the processes of UV-B acclimation that result in altered plant morphology and physiology, we investigated gene expression in different organs of maize at several UV-B fluence rates and exposure times.

Results

Microarray hybridization was used to assess UV-B responses in directly exposed maize organs and organs shielded by a plastic that absorbs UV-B. After 8 hours of high UV-B, the abundance of 347 transcripts was altered: 285 were increased significantly in at least one organ and 80 were downregulated. More transcript changes occurred in directly exposed than in shielded organs, and the levels of more transcripts were changed in adult compared to seedling tissues. The time course of transcript abundance changes indicated that the response kinetics to UV-B is very rapid, as some transcript levels were altered within 1 hour of exposure.

Conclusions

Most of the UV-B regulated genes are organ-specific. Because shielded tissues, including roots, immature ears, and leaves, displayed altered transcriptome profiles after exposure of the plant to UV-B, some signal(s) must be transmitted from irradiated to shielded tissues. These results indicate that there are integrated responses to UV-B radiation above normal levels. As the same total UV-B irradiation dose applied at three intensities elicited different transcript profiles, the transcriptome changes exhibit threshold effects rather than a reciprocal dose-effect response. Transcriptome profiling highlights possible signaling pathways and molecules for future research.

Gene expression profiling in response to ultraviolet radiation in maize genotypes with varying flavonoid content

Microarray hybridization was used to assess acclimation responses to four UV regimes by near isogenic maize (Zea mays) lines varying in flavonoid content. We found that 355 of the 2,500 cDNAs tested were regulated by UV radiation in at least one genotype. Among these, 232 transcripts are assigned putative functions, whereas 123 encode unknown proteins. UV-B increased expression of stress response and ribosomal protein genes, whereas photosynthesis-associated genes were down-regulated; lines lacking UV-absorbing pigments had more dramatic responses than did lines with these pigments, confirming the shielding role of these compounds. Sunlight filtered to remove UV-B or UV-B plus UV-A resulted in significant expression changes in many genes not previously associated with UV responses. Some pathways regulated by UV radiation are shared with defense, salt, and oxidative stresses; however, UV-B radiation can activate additional pathways not shared with other stresses.

Genomic Structure of the Cucumber CPD Photolyase Gene

Light-dependent transcriptional activation of the photolyase gene imparts UVB tolerance to a plant. In the present study, the cucumber CPD photolyase gene (CsPHR) was isolated from a genomic DNA library and its genomic structure was scrutinized. As a result, putative light-responsive cis-acting elements were found in the CsPHR promoter.

Rice UV-damaged DNA binding protein homologues are most abundant in proliferating tissues

Ultraviolet-damaged DNA binding protein (UV-DDB) is an important factor involved in DNA repair. To study the role of UV-DDB, we attempted to obtain the cDNA and the protein of a plant UV-DDB. We succeeded in isolating both genes for UV-DDB subunits from rice (Oryza sativa cv. Nipponbare), designated as OsUV-DDB1 and OsUV-DDB2. OsUV-DDB2 (65 kDa) was much larger than human UV-DDB2, but immunoprecipitation and gel mobility shift assay suggested that OsUV-DDB2 is a plant counterpart of UV-DDB2. The transcripts were expressed in proliferating tissues such as the meristem, but were detected at only low levels in the mature leaves, although the leaves are strongly exposed to UV. These transcripts were induced in the meristem after UV-irradiation. The expression levels of OsUV-DDB were significantly reduced when cell proliferation was temporarily halted. These results indicated that the level of OsUV-DDB expression is correlated with cell proliferation, and its expression may be required mostly for DNA repair in DNA replication.

Characterization of DNA polymerase delta from a higher plant, rice (Oryza sativa L.)

DNA polymerase delta (pol delta), which is comprised of at least two essential subunits, is an important enzyme involved in DNA replication and repair. We have cloned and characterized both the catalytic and small subunits of pol delta from rice (Oryza sativa L. cv. Nipponbare). The open reading frames of OsPoldelta1 and delta2 encoded a predicted product of 1105 amino acid residues with a molecular weight of 124 kDa for OsPoldelta1, and of 429 residues with a molecular weight of 48 kDa for OsPoldelta2. Northern blotting analysis indicated that OsPoldelta1 and delta2 transcripts were expressed strongly in proliferating tissues such as shoot apical meristem. The expression patterns of both subunits in the organs were slightly different. Therefore, we analyzed the spatial distribution pattern of OsPoldelta1 transcripts by in situ hybridization. In the shoot apex, OsPoldelta1 mRNA was abundant in the shoot apical meristem. In the roots, the OsPoldelta1 transcript accumulated at high levels in the root apical meristem. In mature leaves, OsPoldelta1 was induced after UV irradiation, but OsPoldelta2 was not. The amounts of the OsPoldelta1 and delta2 mRNAs in the rice cells changed rapidly during cell proliferation. These results indicated that the levels of OsPoldelta expression are markedly correlated with cell proliferation, and that some of OsPoldelta might have special roles in the leaves.

Homologous recombination and gene targeting in plant cells

Gene targeting has become an indispensable tool for functional genomics in yeast and mouse; however, this tool is still missing in plants. This review discusses the gene targeting problem in plants in the context of general knowledge on recombination and gene targeting. An overview on the history of gene targeting is followed by a general introduction to genetic recombination of bacteria, yeast, and vertebrates. This abridged discussion serves as a guide to the following sections, which cover plant-specific aspects of recombination assay systems, the mechanism of recombination, plant recombination genes, the relationship of recombination to the environment, approaches to stimulate homologous recombination and gene targeting, and a description of two plant systems, the moss Physcomitrella patens and the chloroplast, that naturally have high efficiencies of gene targeting. The review concludes with a discussion of alternatives to gene targeting.

UV-induced DNA damage and repair: a review

Increases in ultraviolet radiation at the Earth's surface due to the depletion of the stratospheric ozone layer have recently fuelled interest in the mechanisms of various effects it might have on organisms. DNA is certainly one of the key targets for UV-induced damage in a variety of organisms ranging from bacteria to humans. UV radiation induces two of the most abundant mutagenic and cytotoxic DNA lesions such as cyclobutane-pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs) and their Dewar valence Isomers. However, cells have developed a number of repair or tolerance mechanism to counteract the DNA damage caused by UV or any other stressors. Photoreactivation with the help of the enzyme photolyase is one of the most important and frequently occurring repair mechanisms in a variety of organisms. Excision repair, which can be distinguished into base excision repair (BER) and nucleotide excision repair (NER), also plays an important role in DNA repair in several organisms with the help of a number of glycosylases and polymerases, respectively. In addition, mechanisms such as mutagenic repair or dimer bypass, recombinational repair, cell-cycle checkpoints, apoptosis and certain alternative repair pathways are also operative in various organisms. This review deals with UV-induced DNA damage and the associated repair mechanisms as well as methods of detecting DNA damage and its future perspectives.

Diurnal change of cucumber CPD photolyase gene (CsPHR) expression and its physiological role in growth under UV-B irradiation

Complementary DNA encoding a putative cyclobutane pyrimidine dimer (CPD)-specific DNA photolyase (CPD photolyase) was isolated from cucumber leaves. The deduced amino acid sequence of the cDNA exhibited high similarity to that of the Arabidopsis CPD photolyase. Transformation with the cDNA restored the impaired photorepair activity of an Escherichia coli mutant, indicating that this cDNA encodes a functional cucumber CPD photolyase (CsPHR). The level of CsPHR transcripts estimated by quantitative RT-PCR as well as the CPD photorepair activity in the cucumber first leaves showed diurnal changes, peaking at 09 : 00 and 12 : 00, respectively. Supplemental UV-B irradiation in the middle of the light period had little effect on the growth of the first leaves, while the supplemental irradiation in the early morning or late afternoon strongly retarded the leaf growth. These results suggest that the diurnal change in CPD photorepair activity, which is presumably regulated by the transcript level of CsPHR, may play an important role in minimizing the growth inhibition due to UV-B irradiation.

Temperature-dependent formation and photorepair of DNA damage induced by UV-B radiation in suspension-cultured tobacco cells

Two photoproducts of DNA damage, i.e. cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs), induced by UV-B radiation in suspension-cultured tobacco cells were quantified by enzyme-linked immunosorbent assay (ELISA) with monoclonal antibodies. CPDs and 6-4PPs were induced in tobacco cells by UV-B radiation. Photorepair of CPDs was faster than that of 6-4PPs. UV-B radiation induces formation of CPDs and 6-4PPs even at 0 degrees C, but low temperature significantly decreases the UV-B-induced (in contrast to UV-C-induced) formation of CPDs and 6-4PPs. Low temperature also retarded the removal of CPDs and 6-4PPs under white light, and almost no photorepair of CPDs and 6-4PPs was detected at 0 degrees C. When purified DNA from tobacco cells grown in darkness was irradiated with UV-B, formation of CPDs and 6-4PPs took place at the same speed at different temperatures. It indicated that formation of CPDs and 6-4PPs induced by UV-B was temperature-independent in a non-cellular system. Based on our results for suspension-cultured tobacco cells, not only the photorepair but also UV-B-induced formation of CPDs and 6-4PPs are temperature-dependent.

Repair of the main UV-induced thymine dimeric lesions within Arabidopsis thaliana DNA: evidence for the major involvement of photoreactivation pathways

The UV-B induced formation of thymine cis-syn cyclobutane dimer and related (6-4) photoproduct was monitored within DNA of cultured cells and plants of Arabidopsis thaliana. This was achieved using a sensitive and accurate HPLC-tandem mass spectrometry assay. It was found that the cyclobutane pyrimidine dimer was formed in a ninefold higher yield than the (6-4) photoproduct. The removal of the lesions was then studied by incubating irradiated cells either in the darkness, under visible light or upon exposure to UV-A radiation. Dark repair of both cyclobutane dimers and (6-4) photoproducts was found to be very ineffective. In contrast, a rapid decrease in the level of photoproducts was observed when UV-B-irradiated cells were exposed to UV-A and, to a lesser extent, to visible light. The removal of (6-4) adducts was found to occur more efficiently. These results strongly suggest that repair of UV-induced photolesions in plants is mainly mediated by photolyases.

Distribution of DNA repair-related ESTs in sugarcane

DNA repair pathways are necessary to maintain the proper genomic stability and ensure the survival of the organism, protecting it against the damaging effects of endogenous and exogenous agents. In this work, we made an analysis of the expression patterns of DNA repair-related genes in sugarcane, by determining the EST (expressed sequence tags) distribution in the different cDNA libraries of the SUCEST transcriptome project. Three different pathways - photoreactivation, base excision repair and nucleotide excision repair - were investigated by employing known DNA repair proteins as probes to identify homologous ESTs in sugarcane, by means of computer similarity search. The results showed that DNA repair genes may have differential expressions in tissues, depending on the pathway studied. These in silico data provide important clues on the potential variation of gene expression, to be confirmed by direct biochemical analysis.

Phenol-oxidizing peroxidases contribute to the protection of plants from ultraviolet radiation stress

We have studied the mechanism of UV protection in two duckweed species (Lemnaceae) by exploiting the UV sensitivity of photosystem II as an in situ sensor for radiation stress. A UV-tolerant Spirodela punctata G.F.W. Meyer ecotype had significantly higher indole-3-acetic acid (IAA) levels than a UV-sensitive ecotype. Parallel work on Lemna gibba mutants suggested that UV tolerance is linked to IAA degradation rather than to levels of free or conjugated IAA. This linkage is consistent with a role for class III phenolic peroxidases, which have been implicated both in the degradation of IAA and the cross-linking of various UV-absorbing phenolics. Biochemical analysis revealed increased activity of a specific peroxidase isozyme in both UV-tolerant duckweed lines. The hypothesis that peroxidases play a role in UV protection was tested in a direct manner using genetically modified tobacco (Nicotiana sylvestris). It was found that increased activity of the anionic peroxidase correlated with increased tolerance to UV radiation as well as decreased levels of free auxin. We conclude that phenol-oxidizing peroxidases concurrently contribute to UV protection as well as the control of leaf and plant architecture.

DNA damage and repair in Arabidopsis thaliana as measured by the comet assay after treatment with different classes of genotoxins

The three protocols of the comet assay A/N, A/A and N/N were for the first time applied to the plant species Arabidopsis thaliana. The purpose of the experiments was to establish conditions for genotoxic exposure causing DNA damage in Arabidopsis nuclei. This is required for comprehensive gene expression profiling with the intention to screen for genes involved in response of Arabidopsis cells to genotoxic stress. Five chemicals belonging to different classes of mutagens (the monofunctional alkylating agents N-methyl-N-nitrosourea and methyl methanesulfonate, the polyfunctional alkylating agent mitomycin C, the radiomimetic bleomycin and the herbicide maleic hydrazide) were tested. Except for maleic hydrazide, dose-dependent increases in DNA damage were found using the A/N comet assay protocol. While a rapid repair of bleomycin-mediated SSBs and DSBs was found, no significant reduction of DNA migration was observed up to 48h after treatment with the monofunctional alkylating agents.

Ultraviolet B radiation enhances a phytochrome-B-mediated photomorphogenic response in Arabidopsis

Ultraviolet B radiation (UV-B, 290-315 nm) can cause damage and induce photomorphogenic responses in plants. The mechanisms that mediate the photomorphogenic effects of UV-B are unclear. In etiolated Arabidopsis seedlings, a daily exposure to 2.5 h of UV-B enhanced the cotyledon opening response induced by a subsequent red light (R) pulse. An R pulse alone, 2.5 h of UV-B terminated with a far-red pulse, or 2.5 h of continuous R caused very little cotyledon opening. The enhancing effect of UV-B increased with fluence rate up to approximately 7.58 micromol m(-2) s(-1); at higher fluence rates the response to UV-B was greatly reduced. The phyA, phyA cry1, and cry1 cry2 mutants behaved like the wild type when exposed to UV-B followed by an R pulse. In contrast, phyB, phyB cry1, and phyB phyA mutants failed to open the cotyledons. Thus, phytochrome B was required for the cotyledon opening response to UV-B --> R treatments, whereas phytochrome A and cryptochromes 1 and 2 were not necessary under the conditions of our experiments. The enhancing effect of low doses of UV-B on cotyledon opening in uvr1 uvr2 and uvr1 uvr3 mutants, deficient in DNA repair, was similar to that found in the wild type, suggesting that this effect of UV-B was not elicited by signals derived from UV-B-induced DNA lesions (cyclobutane pyrimidine dimers and 6-4 photoproducts). We conclude that low doses of UV-B, perceived by a receptor system different from phytochromes, cryptochromes, or DNA, enhance a de-etiolation response that is induced by active phytochrome B.

Mitogen-activated protein kinase phosphatase is required for genotoxic stress relief in Arabidopsis

Genotoxic stress activates complex cellular responses allowing for the repair of DNA damage and proper cell recovery. Although plants are exposed constantly to increasing solar UV irradiation, the signaling cascades activated by genotoxic environments are largely unknown. We have identified an Arabidopsis mutant (mkp1) hypersensitive to genotoxic stress treatments (UV-C and methyl methanesulphonate) due to disruption of a gene that encodes an Arabidopsis homolog of mitogen-activated protein kinase phosphatase (AtMKP1). Growth of the mkp1 mutant under standard conditions is indistinguishable from wild type, indicating a stress-specific function of AtMKP1. MAP kinase phosphatases (MKPs), the potent inactivators of MAP kinases, are considered important regulators of MAP kinase signaling. Although biochemical data from mammalian cell cultures suggests an involvement of MKPs in cellular stress responses, there is no in vivo genetic support for this view in any multicellular organism. The genetic and biochemical data presented here imply a central role for a MAP kinase cascade in genotoxic stress signaling in plants and indicate AtMKP1 to be a crucial regulator of the MAP kinase activity in vivo, determining the outcome of the cellular reaction and the level of genotoxic resistance.