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E Babiychuk

Publications and source records attributed to E Babiychuk.

17 recordsLinked to original sources
PubMed2001

N-terminal domains of plant poly(ADP-ribose) polymerases define their association with mitotic chromosomes.

Poly(ADP-ribos)ylation is a reversible protein modification that in higher plants is catalyzed by two structurally different poly(ADP-ribose) polymerases, App and Zap. In vivo imaging of green-fluorescent protein (GPF) fusions showed that both Zap and App were associated with chromatin through the cell cycle progression. The in vivo behaviour of the App-GFP protein fusions can be attributed to the activity of two NASA motifs that mediate protein-protein interactions and nucleic acid binding. Expression of Zap deletion variants revealed that both Zn fingers and helix-turn-helix domains contributed to the association with chromosomes, whereas the localization in the nucleoplasm was mostly determined by the Zn fingers. The results highlight novel properties of protein sequences found in plant poly(ADP-ribose) polymerases and suggest important functions for this class of nuclear enzymes in chromosome dynamics.

Amino Acid Sequence↗
PubMed2001

A mutation of the mitochondrial ABC transporter Sta1 leads to dwarfism and chlorosis in the Arabidopsis mutant starik.

A mutation in the Arabidopsis gene STARIK leads to dwarfism and chlorosis of plants with an altered morphology of leaf and cell nuclei. We show that the STARIK gene encodes the mitochondrial ABC transporter Sta1 that belongs to a subfamily of Arabidopsis half-ABC transporters. The severity of the starik phenotype is suppressed by the ectopic expression of the STA2 homolog; thus, Sta1 function is partially redundant. Sta1 supports the maturation of cytosolic Fe/S protein in Deltaatm1 yeast, substituting for the ABC transporter Atm1p. Similar to Atm1p-deficient yeast, mitochondria of the starik mutant accumulated more nonheme, nonprotein iron than did wild-type organelles. We further show that plant mitochondria contain a putative l-cysteine desulfurase. Taken together, our results suggest that plant mitochondria possess an evolutionarily conserved Fe/S cluster biosynthesis pathway, which is linked to the intracellular iron homeostasis by the function of Atm1p-like ABC transporters.

Arabidopsis↗
PubMed2000

CEO1, a new protein from Arabidopsis thaliana, protects yeast against oxidative damage.

The Saccharomyces cerevisiae strain WYT, deficient in the YAP1 transcription factor, was used in a molecular screen to identify genes from Arabidopsis thaliana that could overcome the oxidative stress-sensitive phenotype of these yeast cells. A cDNA named CEO1 increased the tolerance to oxidative damage caused by tert-butylhydroperoxide of both the Yap1(-) mutant and the wild-type yeast. Additionally, in Yap1(-) yeast, CEO1 also induced cross-tolerance to oxidative damage caused by hydrogen peroxide and diamide. CEO1 was assigned as being part of a small gene family that, until now, is exclusively restricted to plants. In Arabidopsis, CEO1 was produced in all organs, especially in roots and stems. By using the yeast two-hybrid system, proteins that specifically interact with CEO1 in yeast were identified, and putative DNA-binding proteins were consistently recovered.

Amino Acid Sequence↗
PubMed2000

Crystallization and preliminary X-ray crystallographic analysis of NADPH: azodicarbonyl/quinone oxidoreductase, a plant zeta-crystallin.

Arabidopsis thaliana P1 protein was crystallized using the hanging drop vapor-diffusion method in 0.1 M piperazine-1, 4-bis(2-ethanesulfonic acid) buffer, containing 14% polyethylene glycol 6000 and 0.2 M magnesium acetate at pH 6.5 and 20 degrees C. The crystals are orthorhombic and belong to the space group P2(1)2(1)2(1) with unit cell dimensions of a=49.8, b=122.4 and c=149. 9 A. The diffraction data up to 2.9 A were collected by a multiwire area detector.

Alkanesulfonic Acids↗
PubMed2000

A novel NADPH:diamide oxidoreductase activity in arabidopsis thaliana P1 zeta-crystallin.

The zeta-crystallin (ZCr) gene P1 of Arabidopsis thaliana, known to confer tolerance toward the oxidizing drug 1,1'-azobis(N, N-dimethylformamide) (diamide) to yeast [Babiychuk, E., Kushnir, S., Belles-Boix, E., Van Montagu, M. & Inzé, D. (1995) J. Biol. Chem. 270, 26224], was expressed in Escherichia coli to characterize biochemical properties of the P1-zeta-crystallin (P1-ZCr). Recombinant P1-ZCr, a noncovalent dimer, showed NADPH:quinone oxidoreductase activity with specificity to quinones similar to that of guinea-pig ZCr. P1-ZCr also catalyzed the divalent reduction of diamide to 1,2-bis(N,N-dimethylcarbamoyl)hydrazine, with a kcat comparable with that for quinones. Two other azodicarbonyl compounds also served as substrates of P1-ZCr. Guinea-pig ZCr, however, did not catalyze the azodicarbonyl reduction. Hence, plant ZCr is distinct from mammalian ZCr, and can be referred to as NADPH:azodicarbonyl/quinone reductase. The quinone-reducing reaction was accompanied by radical chain reactions to produce superoxide radicals, while the azodicarbonyl-reducing reaction was not. Specificity to NADPH, as judged by kcat/Km, was > 1000-fold higher than that to NADH both for quinones and diamide. N-Ethylmaleimide and p-chloromercuribenzoic acid inhibited both quinone-reducing and diamide-reducing activities. Both NADPH and NADP+ suppressed the inhibition, but NADH did not, suggesting that sulfhydryl groups reside in the binding site for the phosphate group on the adenosine moiety of NADPH. The diamide-reducing activity of P1-ZCr accounts for the tolerance of P1-overexpressing yeast to diamide. Other possible physiological functions of P1-ZCr in plants are discussed.

Amino Acid Sequence↗
PubMed1998

The involvement of poly(ADP-ribose) polymerase in the oxidative stress responses in plants.

In plants many biotic and abiotic stresses can cause secondary oxidative stress. Earlier work showed that, depending on the severity of the oxidative stress, plants can activate either cell protective genes or programmed cell death (PCD). Poly(ADP-ribose) polymerase (PARP) has been implicated as one of the enzymes in the apoptotic pathways induced by DNA damaging agents or oxidative stress. We show that in cultured soybean cells, PARP is involved in responses to mild and severe oxidative stresses, by mediating DNA repair and PCD processes, respectively. Addition of PARP inhibitors reduced the degree of cell death triggered by H2O2. Two windows of NAD consumption after H2O2 treatment were detected. Experiments with transient overexpression of Arabidopsis PARP cDNA promoted DNA repair and inhibited cell death caused by mild oxidative stress. However, following severe stress PARP overexpression increased cell death. Expression of antisense PARP produced the opposite effects: an increase in DNA nicks and inhibition of cell death at high, but not mild doses of H2O2.

Apoptosis↗
PubMed1998

Higher plants possess two structurally different poly(ADP-ribose) polymerases.

One of the immediate reactions of the mammalian cell to many environmental stresses is a massive synthesis of poly(ADP-ribose), catalyzed by poly(ADP-ribose) polymerase (PARP). Most of the biological functions attributed to PARP are inferred from experimentation with mammalian cells. In plants, the biology of PARP may be more complicated and diverse than was previously thought. Two poly(ADP-ribose) polymerase homologues were found in plants, the classical Zn-finger-containing polymerase (ZAP) and the structurally non-classical PARP proteins (APP and NAP), which lack the characteristic N-terminal Zn-finger domain. By enzymatic and cytological experiments the recombinant APP protein was shown to be located in the nucleus and to possess DNA-dependent poly(ADP-ribose) polymerase activity in yeast. The nuclear localization was further confirmed by the analysis of transgenic tobacco plants that expressed a translational gene fusion between APP and the bacterial beta-glucuronidase. The app promoter was transcriptionally up-regulated in cells pre-determined to die because of deficiency in a DNA ligase I.

Amino Acid Sequence↗
PubMed1997

Efficient gene tagging in Arabidopsis thaliana using a gene trap approach.

Large quantities of DNA sequence information about plant genes are rapidly accumulating in public databases, but to progress from DNA sequence to biological function a mutant allele for each of the genes ideally should be available. Here we describe a gene trap construct that allowed us to disrupt transcribed genes with a high efficiency in Arabidopsis thaliana. In the T-DNA vector used, the expression of a bacterial reporter gene coding for neomycin phosphotransferase II (nptII) depends on the in vivo generation of a translation fusion upon the T-DNA integration into the Arabidopsis genome. Analysis of 20 selected transgenic lines showed that 12 lines are T-DNA insertion mutants. The disrupted genes analyzed encoded ribosomal proteins (three lines), aspartate tRNA synthase, DNA ligase, basic-domain leucine zipper DNA binding protein, ATP-binding cassette transporter, and five proteins of unknown function. Four tagged genes were new for Arabidopsis. The results presented here suggest that gene trapping, using nptII as a reporter gene, can be as high as 80% and opens novel perspectives for systematic gene tagging in A. thaliana.

Arabidopsis↗
PubMed1996

Human foetal lung (IMR-90) cells: myofibroblasts with smooth muscle-like contractile properties.

Single cells displaying many characteristics in common with smooth muscle are now being identified in many organs. Although their origin remains elusive, they are nonetheless known to play a major role in fibroproliferative diseases and stromal reactions by virtue of their contractile properties. We have investigated the contractile properties and expression of smooth muscle-associated proteins in such a cell line derived from human foetal lung (IMR-90). For almost two decades, these cells have served as model fibroblasts in a wide variety of studies. And yet, IMR-90 cells manifest many features characteristic of differentiated smooth muscle cells: they exhibit the same elongated, slender form and the strikingly regular, longitudinal alignment of their actin-attachment sites, which are indispensable for coordinated contraction. Moreover, these adhaerens junctions also contain metavinculin, the smooth muscle analogue of vinculin, the stable expression of which has not previously been demonstrated in cultured cells. Since sm 22, as well as the smooth muscle-associated alpha-actin isoform and calponin are also expressed, IMR-90 cells must now be classified as myofibroblasts. When cultivated on a rubbery silicon surface, IMR-90 cells respond to stimulation with a rate of contraction which is considerably faster than that exhibited by fibroblasts derived from other established lines. Taken together, the regular longitudinal orientation of the adhaerens junctions, the stable expression of metavinculin, and the rapid speed of shortening in IMR-90 cells suggest, by implication, that the periodicity of actin attachment sites is a fundamental determinant of contractile efficiency in smooth muscle cells; this spacing may be mediated by metavinculin.

3T3 Cells↗
PubMed1995

Alterations in chlorophyll a/b binding proteins in Solanaceae cybrids.

In this study we have constructed a number of plants (cybrids), in which the nuclear genome of Nicotiana plumbaginifolia is combined with the plastome of Atropa belladonna, or the nuclear genome of N. tabacum with plastomes of Lycium barbarum, Scopolia carniolica, Physochlaine officinalis or Nolana paradoxa. Our biochemical and immunological analyses prove that in these cybrids the biogenesis of the chlorophyll a/b binding proteins (CAB) of the light harvesting complex II (LHCII) is altered. Besides normal sized CAB polypeptides of 27, 25.5 and 25 kDa, which become less abundant, the cybrids analyzed have additional polypeptides of 26, 24.5 and 24 kDa. Direct protein micro-sequencing showed that at least two truncated 26 kDa CAB polypeptides in plant cells containing a nucleus of N. plumbaginifolia and plastids of A. belladonna are encoded by the type 1 Lhcb genes. These polypeptides are 11-12 amino acids shorter at the N-terminus than the expected size. Based on the available data we conclude that the biogenesis of the LHCII in vivo may depend on plastome-encoded factor(s). These results suggest that plastome-encoded factors that cause specific protein degradation and/or abnormal processing might determine compartmental genetic incompatibility in plants.

Amino Acid Sequence↗
PubMed1995

Molecular characterization of a putative Arabidopsis thaliana copper transporter and its yeast homologue.

At the molecular level, little is known about the transport of copper across plant membranes. We have isolated an Arabidopsis thaliana cDNA by complementation of a mutant (ctr1-3) of Saccharomyces cerevisiae defective in high affinity copper uptake. This cDNA codes for a highly hydrophobic protein (COPT1) of 169 amino acid residues and with three putative transmembrane domains. Most noteworthy, the first 44 residues display significant homology to the methionine- and histidine-rich copper binding domain of three bacterial copper binding proteins, among these a copper transporting ATPase. Mutant yeast cells expressing COPT1 exhibit nearly wild type behavior with regard to growth on a nonfermentable carbon source and resistance to copper and iron starvation. Expression of COPT1 is also associated with an increased sensitivity to copper toxicity. Additionally, COPT1 shows significant homology to an open reading frame of 189 amino acid residues on yeast chromosome VIII. This gene (CTR2) may encode an additional yeast metal transporter able to mediate the uptake of copper. A mutation in CTR2 displays a higher level of resistance to toxic copper concentrations. Overexpression of CTR2 provides increased resistance to copper starvation and is also associated with an increased sensitivity to copper toxicity. The amino acid sequence of CTR2, like Arabidopsis COPT1, contains three potential transmembrane domains. Taken together, the data suggest that a plant metal transporter, which is most likely involved in the transport of copper, has been identified.

Amino Acid Sequence↗
PubMed1995

Characterization of Arabidopsis thaliana cDNAs that render yeasts tolerant toward the thiol-oxidizing drug diamide.

Diamide oxidizes cellular thiols and induces oxidative stress. To isolate plant genes which may, when overexpressed, increase tolerance of plants toward oxidative damage, an in vivo diamide tolerance screening in yeasts was used. An Arabidopsis cDNA library in a yeast expression vector was used to transform a yeast strain with intact antioxidant defense. Cells from approximately 10(5) primary transformants were selected for resistance to diamide. Three Arabidopsis cDNAs which confer diamide tolerance were isolated. This drug tolerance was specific and no cross tolerance toward hydroperoxides was found. One cDNA (D3) encodes a polypeptide which has an amino-terminal J domain characteristic of a divergent family of DnaJ chaperones. Another (D18) encodes a putative dTDP-D-glucose 4,6-dehydratase. Surprisingly, the third cDNA (D22) encodes a plant homolog of gamma-glutamyltransferases. It would have been difficult to predict that the expression of those genes would lead to an improved survival under conditions of depletion of cellular thiols. Hence, we suggest that this cloning approach may be a useful contribution to the isolation of plant genes that can help to cope with oxidative stress.

Amino Acid Sequence↗
PubMed1995

Arabidopsis thaliana NADPH oxidoreductase homologs confer tolerance of yeasts toward the thiol-oxidizing drug diamide.

To isolate new plant genes involved in the defense against oxidative stress, an Arabidopsis cDNA library in a yeast expression vector was transformed into a yeast strain deficient in the YAP1 gene, which encodes a b-Zip transcription factor and regulates general stress response in yeasts. Cells from approximately 10(5) primary transformants were subjected to a tolerance screen toward the thiol-oxidizing drug diamide, which depletes the reduced glutathione in the cell. Four types of Arabidopsis cDNAs were isolated. Three of these cDNAs (P1, P2, and P4) belong to a plant zeta-crystallin family and P3 is an Arabidopsis homolog of isoflavonoid reductases. As such, all four isolated cDNAs are homologous to NADPH oxidoreductases. P1, P2, and P3 steady-state mRNAs accumulated rapidly in Arabidopsis plants under various oxidative stress conditions, such as treatment with paraquat, t-butylhydroperoxide, diamide, and menadione. The data suggested that proteins encoded by the isolated cDNAs play a distinct role in plant antioxidant defense and are possibly involved in NAD(P)/NAD(P)H homeostasis.

Amino Acid Sequence↗
PubMed1995

Characterization of an Arabidopsis thaliana cDNA homologue to animal poly(ADP-ribose) polymerase.

A full-length Arabidopsis thaliana cDNA (app) encoding a protein with high similarity (about 60%) to the catalytic domain of vertebrate poly(ADP-ribose) polymerase (PARP; EC 2.4.2.30) has been cloned. The N-terminal extension of the Arabidopsis protein shows similarities with domains of different nuclear and DNA binding proteins in agreement with nuclear localization and putative function of a plant PARP. APP is encoded by a single gene mapped at the top of chromosome 4 of the Arabidopsis genome and mRNA is abundant in cell suspension culture compared to its accumulation in whole plant.

Amino Acid Sequence↗
PubMed1994

The Arabidopsis thaliana apurinic endonuclease Arp reduces human transcription factors Fos and Jun.

An Arabidopsis thaliana cDNA encoding an analogue, referred to as Arp for apurinic endonuclease-redox protein, of the human redox factor REF has been cloned. Arp stimulates in vitro DNA-binding activity of the human transcription factor Jun and Fos by the reduction of a cysteine residue located in the DNA-binding domain. Based on amino acid sequence homology, this redox activity is probably confined to the small internal domain of the Arp protein. In analogy to REF, we show that the Arabidopsis Arp protein also functions as an apurinic/apyrimidinic class II endonuclease. This base-free endonuclease activity resides in the carboxyl-terminal domain, and this part of the protein has significant sequence similarity to bacterial (Escherichia coli exonuclease III and Streptococcus pneumoniae exonuclease A) and animal (Drosophila Rrp1 and human REF/HAP) apurinic/apyrimidinic endonucleases. The amino-terminal domain of the Arp protein is highly charged and apparently increases the affinity of the protein for DNA. Therefore, the Arabidopsis Arp protein is multifunctional and may be involved both in DNA repair and in the regulation of transcription.

Arabidopsis↗
PubMed1991

Nucleo-cytoplasmic incompatibility in cybrid plants possessing an Atropa genome and a Nicotiana plastome.

Twenty-nine cybrids possessing an Atropa belladonna nuclear genome and a Nicotiana tabacum plastome were selected from two independent protoplast fusion experiments. In contrast to the previously described reciprocal, green and fertile cybrids with a Nicotiana nuclear genome and an Atropa plastome (Kushnir et al. 1987), the plants obtained were totally chlorophyll-deficient. An Atropa nuclear genome and a Nicotiana plastome from these chlorophyll-deficient cybrids were combined with an Atropa or a Scopolia plastome and a Nicotiana nuclear genome, respectively, in control fusion experiments. All of these nuclear genome/plastome combinations gave rise to normal, green plants. Therefore, we conclude that an N. tabacum plastome is incompatible with an A. belladonna nuclear genome.

Amylases↗