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PubMed2005

Importance of sequence and structural elements within a viral replication repressor.

Efficient replication of plus-strand RNA viruses requires a 3' proximal core promoter and an increasingly diverse inventory of supporting elements such as enhancers, repressors, and 5' terminal sequences. While core promoters have been well characterized, much less is known about structure-functional relationships of these supporting elements. Members of the genus Carmovirus family Tombusviridae contain a hairpin (H5) proximal to the core promoter that functions as a repressor of minus-strand synthesis in vitro through an interaction between its large symmetrical internal loop (LSL) and 3' terminal bases. Turnip crinkle virus satellite RNA satC with the H5 of carmovirus Japanese iris necrosis virus or Cardamine chlorotic fleck virus (CCFV) did not accumulate to detectable levels even though 3' end base-pairing would be maintained. Replacement of portions of the satC H5 with analogous portions from CCFV revealed that the cognate LSL and lower stem were of greater importance for satC accumulation than the upper stem. In vivo selex of the H5 upper stem and terminal GNRA tetraloop revealed considerable plasticity in the upper stem, including the presence of three- to six-base terminal loops, allowed for H5 function. In vivo selex of the lower stem revealed that both a stable stem and specific base pairs contributed to satC fitness. Surprisingly, mutations in H5 had a disproportionate effect on plus-strand accumulation that was unrelated to the stability of the mutant plus-strands. In addition, fitness to accumulate in plants did not always correlate with enhanced ability to accumulate in protoplasts, suggesting that H5 may be multifunctional.

Base Sequence↗
PubMed2000

Growth and stomatal responses of temperate meadow species to enhanced levels of UV-A and UV-B+A radiation in the natural environment.

Some responses of various meadow species to enhanced UV-radiation of the natural daylight spectrum are described together with the experimental protocol employed. Growth responses to supplementary UV-B+A are mostly inhibitory when compared to the ambient daylight treatment for Bellis perennis, Cardamine pratensis, Cynosurus critatus and Ranunculus ficaria. However, the response of UV-A treatment compared to that of the UV-B+A varies in significance according to the species and parameter investigated. The pertinence of the ambient and UV-A treatment to data interpretation is discussed. Stomatal conductance of B. perennis was measured throughout the 24 h cycle. Although no significant difference could be found between the stomatal conductance of UV and ambient treated plants during the hours of daylight, at night it was found that the UV-B+A treated plants were unable to achieve the same degree of closure as the ambient treated plants. UV-damage and growth responses could alter the diversity of the meadow ecosystem and these effects could be exacerbated by water loss.

Asteraceae↗
PubMed2005

Extinction dynamics in experimental metapopulations.

Metapopulation theory provides a framework for understanding population persistence in fragmented landscapes and as such has been widely used in conservation biology to inform management of fragmented populations. However, classical metapopulation theory [Levins, R. (1970) Lect. Notes Math. 2, 75-107] ignores metapopulation structure and local population dynamics, both of which may affect extinction dynamics. Here, we investigate metapopulation dynamics in populations that are subject to different migration rates by using experimental metapopulations of the annual plant Cardamine pensylvanica. As predicted by classical metapopulation theory, connected populations persisted longer than did isolated populations, but the relationship between migration and persistence time was nonlinear. Extinction risk sharply increased as the distance between local populations increased above a threshold value that was consistent with stochastic simulations and calculation of metapopulation capacity [Hanski, I. & Ovaskainen, O. (2000) Nature 404, 755-758]. In addition, the most connected metapopulations did not have the highest persistence levels. Stochastic simulations indicated an increase in extinction risk with the highest migration rates. Moreover, calculation of population coherence [Earn, D. J. D., Levin, S. A. & Rohani, P. (2000) Science 290, 1360-1364], a metric that predicts synchronous cycles, indicated that continuous populations should cycle in phase, resulting in an increased extinction risk. Determining empirically the optimal migration level to improve survival chances will be challenging for any natural population. Migration rates that would not increase migration above the threshold value would be ineffectual, but migration rates that would homogenize local densities could increase the risk of coherent oscillations and enhance extinction risk.

Ecology↗
PubMed2001

Bioindication of heavy metals with aquatic macrophytes: the case of a stream polluted with power plant sewages in Poland.

The Kozi Brod (left tributary of the Biala Przemsza, east of Katowice) flows in a highly industrial coal-mining area dominated by the power plant of Siersza. Concentrations of the microelements nickel (Ni), chromium (Cr), cobalt (Co), zinc (Zn), manganese (Mn), lead (Pb), cadmium (Cd), copper (Cu), barium (Ba), aluminum (Al), vanadium (V), and strontium (Sr), as well as the macronutrients nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), iron (Fe), and sulfur (S), were measured in water and plants of the Kozi Brod. The collected plants were: Myosotis palustris L. Nathorst, Galium palustre L., Mentha rotundifolia L. Huds., Mentha aquatica L., Berula erecta (Huds.) Coville, Cardamine amara L., Epilobium angustifolium L., Geranium palustre L., Lysimachia vulgaris L., Crepis paludosa L. Much., Calitriche verna L., Solanum dulcamara L., and the aquatic moss Hygrohypnum ochraceum (Turn.) Loesk. These plants were used to evaluate the spatial distribution of elements in the Kozi Brod and contained elevated levels of Co, Cd, Zn, Ni, Mn, Al, Pb, and Cu. Significant correlations between concentrations of Cd, Zn, and Mn in water and plants indicate the potential of these species for pollution monitoring.

Coal Mining↗
PubMed2005

Evolution of the trnF(GAA) gene in Arabidopsis relatives and the brassicaceae family: monophyletic origin and subsequent diversification of a plastidic pseudogene.

Recently, we used the 5'-trnL(UAA)-trnF(GAA) region of the chloroplast DNA for phylogeographic reconstructions and phylogenetic analysis among the genera Arabidopsis, Boechera, Rorippa, Nasturtium, and Cardamine. Despite the fact that extensive gene duplications are rare among the chloroplast genome of higher plants, within these taxa the anticodon domain of the trnF(GAA) gene exhibit extensive gene duplications with one to eight tandemly repeated copies in close 5' proximity of the functional gene. Interestingly, even in Arabidopsis thaliana we found six putative pseudogenic copies of the functional trnF gene within the 5'-intergenic trnL-trnF spacer. A reexamination of trnL(UAA)-trnF(GAA) regions from numerous published phylogenetic studies among halimolobine, cardaminoid, and other cruciferous taxa revealed not only extensive trnF gene duplications but also favor the hypothesis about a single origin of trnF pseudogene formation during evolution of the Brassicaceae family 16-21 MYA. Conserved sequence motifs from this tandemly repeated region are codistributed nonrandomly throughout the plastome, and we found some similarities with a DNA sequence duplication in the rps7 gene and its adjacent spacer. Our results demonstrate the potential evolutionary dynamics of a plastidic region generally regarded as highly conserved and probably cotranscribed and, as shown here for several genera among cruciferous plants, greatly characterized by parallel gains and losses of duplicated trnF copies.

Arabidopsis↗
PubMed2026

DNA-binding activity of PIF7 links phytochrome B signaling to plant responses to vegetation proximity.

PHYTOCHROME INTERACTING FACTORs (PIFs) are transcription factors that act as central signaling hubs in light-regulated processes. All PIFs contain an active phytochrome B-binding motif and a DNA-binding basic helix-loop-helix domain. In the shade-avoider Arabidopsis thaliana, PIF7 is a major promoter of hypocotyl elongation in response to vegetation proximity, becoming active when released from phytochrome B via its active phytochrome B-binding motif. Here we show that PIF7 promotes seedling elongation in other species, including the shade-avoider tomato and the shade-tolerant Cardamine hirsuta, suggesting that PIF7 has retained some of its key functional domains across diverse plants. Through complementation analyses using PIF7 variants lacking either the active phytochrome B-binding or basic helix-loop-helix domain, we demonstrate that, unlike PIF3, PIF7 versions unable to bind phytochrome B remain active regardless of light conditions, whereas loss of DNA-binding capacity fully disrupts PIF7 function. Our results further suggest that phytochrome B interaction imposes a dual regulatory control over PIF7, modulating both its abundance and its phosphorylation state (ie its ability to bind and regulate target genes).

Phytochrome B↗
PubMedDate not supplied

Open reading frames of turnip crinkle virus involved in satellite symptom expression and incompatibility with Arabidopsis thaliana ecotype Dijon.

Carmoviruses are single-stranded, single component RNA viruses that include turnip crinkle virus (TCV) and the recently discovered cardamine chlorotic fleck virus (CCFV). Full-length, biologically active cDNAs were constructed for the TCV-M isolate and the Blue Lake isolate of CCFV. Using chimeric viruses constructed between isolates of TCV that produce mild or severe symptoms when coinoculated with a virulent satellite RNA, a Glu residue at position 1,144 in the polymerase open reading frame was identified as being involved in satellite-mediated symptom expression. To analyze viral determinants involved in resistance, chimeric viruses with precisely exchanged open reading frames were produced between TCV, which does not infect the Arabidopsis thaliana ecotype Dijon (Di-0), and CCFV, which can infect Di-0, TCV with the coat protein of CCFV was able to systemically infect Di-0 although whole plant hybridizations revealed that the hybrid virus spread more slowly than either of the two parental viruses. These results indicate that the two parental viruses. These results indicate that the coat protein is an important viral determinant in the resistance of Di-0 to TCV.

Amino Acid Sequence↗
PubMed1995

Symptom attenuation by a normally virulent satellite RNA of turnip crinkle virus is associated with the coat protein open reading frame.

Many satellite RNAs (sat-RNAs) can attenuate or intensify the symptoms produced by their helper virus. Sat-RNA C, associated with turnip crinkle virus (TCV), was previously found to intensify the symptoms of TCV on all plants in which TCV produced visible symptoms. However, when the coat protein open reading frame (ORF) of TCV was precisely exchanged with that of cardamine chlorotic fleck virus, sat-RNA C attenuated the moderate symptoms of the chimeric virus when Arabidopsis plants were coinoculated with the chimeric virus. Symptom attenuation was correlated with a reduction in viral RNA levels in inoculated and uninoculated leaves. In protoplasts, the presence of sat-RNA C resulted in a reduction of approximately 70% in the chimeric viral genomic RNA at 44 hr postinoculation, whereas the sat-RNA wa consistently amplified to higher levels by the chimeric virus than by wild-type TCV. TCV with a deletion of the coat protein ORF also resulted in a similar increase in sat-RNA C levels in protoplasts, indicating that the TVC coat protein, or its ORF, downregulates the synthesis of sat-RNA C. These results suggest that the coat protein or its ORF is a viral determinant for symptom modulation by sat-RNA C, and symptom attenuation is at least partly due to inhibition of virus accumulation.

Arabidopsis↗
PubMed1997

Satellite RNA-mediated resistance to turnip crinkle virus in Arabidopsis involves a reduction in virus movement.

Satellite RNAs (sat-RNAs) are parasites of viruses that can mediate resistance to the helper virus. We previously showed that a sat-RNA (sat-RNA C) of turnip crinkle virus (TCV), which normally intensifies symptoms of TCV, is able to attenuate symptoms when TCV contains the coat protein (CP) of cardamine chlorotic fleck virus (TCV-CPCCFV). We have now determined that sat-RNA C also attenuates symptoms of TCV containing an alteration in the initiating AUG of the CP open reading frame (TCV-CPm). TCV-CPm, which is able to move systemically in both the TCV-susceptible ecotype Columbia (Col-0) and the TCV-resistant ecotype Dijon (Di-0), produced a reduced level of CP and no detectable virions in infected plants. Sat-RNA C reduced the accumulation of TCV-CPm by < 25% in protoplasts while reducing the level of TCV-CPm by 90 to 100% in uninoculated leaves of Col-0 and Di-0. Our results suggest that in the presence of a reduced level of a possibly altered CP, sat-RNA C reduces virus long-distance movement in a manner that is independent of the salicylic acid-dependent defense pathway.

Arabidopsis↗
PubMed2000

3'-End stem-loops of the subviral RNAs associated with turnip crinkle virus are involved in symptom modulation and coat protein binding.

Many plant RNA viruses are associated with one or more subviral RNAs. Two subviral RNAs, satellite RNA C (satC) and defective interfering RNA G (diG) intensify the symptoms of their helper, turnip crinkle virus (TCV). However, when the coat protein (CP) of TCV was replaced with that of the related Cardamine chlorotic fleck virus (CCFV), both subviral RNAs attenuated symptoms of the hybrid virus TCV-CP(CCFV). In contrast, when the translation initiation codon of the TCV CP was altered to ACG and reduced levels of CP were synthesized, satC attenuated symptoms while diG neither intensified nor attenuated symptoms. The determinants for this differential symptom modulation were previously localized to the 3'-terminal 100 bases of the subviral RNAs, which contain six positional differences (Q. Kong, J.-W. Oh, C. D. Carpenter, and A. E. Simon, Virology 238:478-485, 1997). In the current study, we have determined that certain sequences within the 3'-terminal stem-loop structures of satC and diG, which also serve as promoters for complementary strand synthesis, are critical for symptom modulation. Furthermore, the ability to attenuate symptoms was correlated with weakened binding of TCV CP to the hairpin structure.

Arabidopsis↗
PubMed1999

Oxidative damage to plant DNA in relation to growth conditions.

In this study we investigated the level of 8-oxo-2'-deoxyguanosine (8-oxodG) in DNA of Cardamine pratensis plants subjected to different growth conditions trying to answer the question whether factors like light and water accessibility or low temperature may have an impact on the total DNA oxidative damage. The level of this modified nucleoside was determined using HPLC coupled to UV absorbance and electrochemical detection (HPLC-UV-EC). We did not observe any statistically significant differences in 8-oxodG level between DNA of etiolated and light exposed plants as well as between DNA of regularly watered and drought-subjected plants. In contrast, we have shown that chilling (1 degree C for 28 h) brings about the increase of 8-oxodG level in DNA.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed2003

The function of the flowering time gene AGL20 is conserved in Crucifers.

The MADS box gene, AGAMOUS-LIKE 20 (AGL20), integrates environmental and endogenous flowering signals in Arabidopsis thaliana. In order to determine if its role is conserved in other plants, we isolated AGL20 orthologs from Brassica campestris, Cardamine flexuosa and Draba nemorosa. The putative amino acid sequences of the orthologs were 94 to 97% identical. We analyzed the flowering phenotype and expression level of the AGL20 ortholog in C. flexuosa, a long day plant that does not respond to vernalization. CaAGL20 was more highly expressed in long days than short days and its expression did not change in response to vernalization, indicating that its expression is correlated with flowering time, as in Arabidopsis. When the Brassica AGL20 ortholog was constitutively expressed in sense and antisense orientations using the 35S cauliflower mosaic virus promoter, some of the sense transgenic plants flowered extremely early and some of the antisense plants exhibited delayed flowering. These results suggest that the role of AGL20 is conserved in Crucifers.

Amino Acid Sequence↗
PubMed2006

Antioxidant activity of wild plants collected in Valsesia, an alpine region of Northern Italy.

A selection of wild plants collected in Valsesia (Northwest Italy) was screened for their in vitro antioxidant activity. Aerial parts of selected plants were dried at room temperature and powdered. Then, four sequential extractions were performed with increasing polarity solvents, i.e. n-hexane, chloroform, chloroform-methanol (9:1, v/v) and methanol. By employing different assays, it was shown that all the methanol extracts of the samples collected were endowed with antioxidant activity, though, as expected, their potency varied according to the different tests. In particular, plants of the Thymus and Achillea genus displayed the highest activity. Given that a diet rich in wild plants is associated with a reduced incidence of degenerative diseases, such as atherosclerosis and cancer, this study suggests that some Valsesia plants could be pharmaceutically exploited.

Achillea↗