Transcriptome profiling reveals similarities and differences in plant responses to cadmium and lead

We analyzed the influence of salts of two heavy metals—lead and cadmium (Pb²⁺ and Cd²⁺) on plants, including plant and root size, plant genome stability as well as global genome expression. Measurement of the metal uptake showed that there was a significantly higher incorporation of Cd than of Pb, 0.6 and 0.15 uM per gram of dry weight, respectively. The analysis of the root length and plant size showed a dose dependent decrease in plants exposed to cadmium. In contrast there was little difference in the size of plants exposed to lead, although there was nearly four-fold increase of the root length. Analysis of the genome stability revealed that cadmium led to a dose dependent increase of homologous recombination whereas lead had no effect.

Analysis of the global genome expression of plants chronically exposed to 50 uM of Cd and Pb revealed 65 and 338 up- and down-regulated genes by Cd and 19 and 76 by Pb, respectively. Interestingly, half of the genes that changed their expression in Pb-treated plants also changed their expression in Cd-treated ones. The greater number of genes regulated by Cd reflects generally higher genome instability of plants as well as higher uptake as compared to Pb.     

Fractionated low-dose radiation exposure leads to accumulation of DNA damage and profound alterations in DNA and histone methylation in the murine thymus

Thymus, an important component of hematopoietic tissue, is a well-documented "target" of radiation carcinogenesis. Both acute and fractionated irradiation result in a high risk of leukemia and thymic lymphoma. However, the exact mechanisms underlying radiation-induced predisposition to leukemia and lymphoma are still unknown, and the contributions of genetic and epigenetic mechanisms in particular have yet to be defined. Global DNA hypomethylation is a well-known characteristic of cancer cells. Recent studies have also shown that tumor cells undergo prominent changes in histone methylation, particularly a substantial loss of trimethylation of histone H4-Lys20 and demethylation of genomic DNA. These losses are considered a universal marker of malignant transformation. In the present study, we investigated the effect of low-dose radiation exposure on the accumulation of DNA lesions and alterations of DNA methylation and histone H4-Lys20 trimethylation in the thymus tissue using an in vivo murine model. For the first time, we show that fractionated whole-body application of 0.5 Gy X-ray leads to decrease in histone H4-Lys20 trimethylation in the thymus. The loss of histone H4-Lys20 trimethylation was accompanied by a significant decrease in global DNA methylation as well as the accumulation of DNA damage as monitored by persistence of histone gammaH2AX foci in the thymus tissue of mice exposed to fractionated irradiation. Altered DNA methylation was associated with reduced expression of maintenance (DNMT1) and, to a lesser extent, de novo DNA methyltransferase DNMT3a in exposed animals. Expression of another de novo DNA methyltransferase DNMT3b was decreased only in males. Irradiation also resulted in approximately 20% reduction in the levels of methyl-binding proteins MeCP2 and MBD2. Our results show the involvement of epigenetic alterations in radiation-induced responses in vivo. These changes may play a role in genome destabilization that ultimately leads to cancer.     

Biomimetic Synthesis of Nanosized Silica Structures on a Substrate with Silicatein

Using atomic force microscopy (AFM), the formation of nanosized silica structures on a substrate, catalyzed by the recombinant silicatein LoSilA1 from the marine sponge Latrunculia oparinae, was studied. It has been shown that at room temperature under neutral conditions, recombinant silicatein immobilized on a mica substrate causes the rapid polycondensation of tetrakis(2-hydroxyethyl) orthosilicate to form spherical particles. Thus, immobilized silicatein may acts as a catalyst in the preparation of ordered silica structures on various surfaces.     

Free Amino Acid Profile in Blood Plasma of Bats (<Emphasis Type="Italic">Myotis dasycneme</Emphasis> Boie, 1825) Exposed to Low Positive and Near-Zero Temperatures

We analyze here for the first time the plasma free amino acid profile in pond bats (Myotis dasycneme Boie, 1825) living in the boreal Ural region and exposed experimentally to low positive and near-zero temperatures during their preparation for hibernation. Pond bats were caught in their mass habitation territory in the Middle Ural near the Smolinsky cave (N 56°28’, E 61°37’) in the third decade of September 2015. Qualitatively, blood plasma in pond bats contains 21 amino acids. In a model experiment carried out on pre-hibernating animals at a regular hibernation temperature (0–2°C), the total plasma pool of free amino acids increased significantly by 42% (irrespective of sex) and reached 1561.4 ± 112.6 μmol/L (p = 0.01). Under these experimental conditions, the fraction of glucogenic amino acids rose by 34% (p = 0.01) and that of essential ones by 80% (p = 0.001). Both in control and experimentally cooled pre-hibernating animals, the plasma was found to lack tryptophan, suggesting its utilization as a substrate in the synthesis of serotonin, a biogenic amine directly involved in the maintenance of hypothermia and hypometabolism in these chiropterans.     

Distribution and conservation of mobile elements in the genus Drosophila

Essentially nothing is known of the origin, mode of transmission, and evolution of mobile elements within the genus Drosophila. To better understand the evolutionary history of these mobile elements, we examined the distribution and conservation of homologues to the P, I, gypsy, copia, and F elements in 34 Drosophila species from three subgenera. Probes specific for each element were prepared from D. melanogaster and hybridized to genomic DNA. Filters were washed under conditions of increasing stringency to estimate the similarity between D. melanogaster sequences and their homologues in other species. The I element homologues show the most limited distribution of all elements tested, being restricted to the melanogaster species group. The P elements are found in many members of the subgenus Sophophora but, with the notable exception of D. nasuta, are not found in the other two subgenera. Copia-, gypsy-, and F-element homologues are widespread in the genus, but their similarity to the D. melanogaster probe differs markedly between species. The distribution of copia and P elements and the conservation of the gypsy and P elements is inconsistent with a model that postulates a single ancient origin for each type of element followed by mating-dependent transmission. The data can be explained by horizontal transmission of mobile elements between reproductively isolated species.      

The Genome of the marine bacterium <Emphasis Type="Italic">Cobetia marina</Emphasis> KMM 296 isolated from the mussel <Emphasis Type="Italic">Crenomytilus grayanus</Emphasis> (Dunker, 1853)

We determined the entire genome sequence of the marine bacterium Cobetia marina KMM 296 de novo, which was isolated from the mussel Crenomytilus grayanus that inhabits the Sea of Japan. The genome that provides the lifestyle of this marine bacterium provides alternative metabolic pathways that are characteristic of the inhabitants of the rhizospheres of terrestrial plants, as well as deep-sea ecological communities (symbiotic and free-living bacteria). The genome of C. marina KMM 296 contains genes that are involved in the metabolism and transport of nitrogen, sulfur, iron, and phosphorus. C. marina strain KMM 296 is a promising source of unique psychrophilic enzymes and essential secondary metabolites.     

Tobacco Mosaic Virus Infection Results in an Increase in Recombination Frequency and Resistance to Viral,Bacterial, and Fungal Pathogens in the Progeny of Infected Tobacco Plants

Our previous experiments showed that infection of tobacco (Nicotiana tabacum) plants with Tobacco mosaic virus (TMV) leads to an increase in homologous recombination frequency (HRF). The progeny of infected plants also had an increased rate of rearrangements in resistance gene-like loci. Here, we report that tobacco plants infected with TMV exhibited an increase in HRF in two consecutive generations. Analysis of global genome methylation showed the hypermethylated genome in both generations of plants, whereas analysis of methylation via 5-methyl cytosine antibodies demonstrated both hypomethylation and hypermethylation. Analysis of the response of the progeny of infected plants to TMV, Pseudomonas syringae, or Phytophthora nicotianae revealed a significant delay in symptom development. Infection of these plants with TMV or P. syringae showed higher levels of induction of PATHOGENESIS-RELATED GENE1 gene expression and higher levels of callose deposition. Our experiments suggest that viral infection triggers specific changes in progeny that promote higher levels of HRF at the transgene and higher resistance to stress as compared with the progeny of unstressed plants. However, data reported in these studies do not establish evidence of a link between recombination frequency and stress resistance.Continuous exposure to stress leads to the evolutionary selection of adaptive traits beneficial in a particular environment. Such selection of the fittest of a population of plants grown under certain environmental conditions is believed to require a long time. However, it is known that plants also possess the ability to acclimate on much shorter time scales. A modification of homeostasis, also termed acclimatization, is a well-documented process that is used for adjusting metabolism to a new environment (Lichtenthaler, 1998; Mullineaux and Emlyn-Jones, 2005).Pathogens represent one of a variety of stresses that plants are constantly exposed to. In nature, the evolution of plant resistance to a particular pathogen, virus, bacterium, or fungus has been the result of constant interactions with said pathogen (McHale et al., 2006; Friedman and Baker, 2007). These interactions lead to a constant plant-pathogen arms race (Ingle et al., 2006).Plants are able to tolerate or resist pathogens in a variety of ways, which could be broadly attributed to mechanisms of innate immunity and actual gene-for-gene-based resistance. The latter one depends on direct or indirect recognition of pathogen avirulence gene products by plant resistance gene products (Whitham et al., 1994; Durrant and Dong, 2004). Pathogen recognition during this incompatible interaction triggers complex events, including a local hypersensitive response that manifests itself as a booster of radical production and activation of the salicylic acid-dependent pathway and necrotic lesions, which working together restrict pathogen spread. It also results in a plant-wide systemic acquired resistance response that provides protection and tolerance to future pathogen attacks (Durrant and Dong, 2004; Park et al., 2007; Vlot et al., 2008).If a functional pathogen resistance gene is absent (compatible interaction), then the interaction between a plant and a pathogen is more ambiguous. How do plants that lack a resistance gene respond to infection? We have previously reported that the compatible interaction between Tobacco mosaic virus (TMV) and tobacco (Nicotiana tabacum ‘SR1’) plants lacking the TMV resistance N gene results in the production of a systemic signal. The signal leads to an increase in the frequency of somatic homologous recombination (HRF; Kovalchuk et al., 2003a). Based on these observations, we hypothesized that these genomic changes could be inherited. Indeed, we found that the progeny of infected SR1 tobacco plants exhibited a higher frequency of RFLPs at the loci that have similarity (more than 60%) to the Leu-rich repeat region of the N gene (Boyko et al., 2007).Although several reports have shown an increase in genome instability in plants exposed to pathogens and pathogen elicitors (Lucht et al., 2002; Kovalchuk et al., 2003a; Molinier et al., 2006; Boyko et al., 2007), many questions still remained unanswered. What is the mechanism of occurrence of a pathogen-induced systemic increase in HRF? What is the mechanism of inheritance of high-frequency homologous recombination? Are elevated levels of HRF maintained throughout generations? What other changes occur in progeny of infected plants?Here, we attempted to answer the above questions by analyzing two consecutive progenies of TMV-infected tobacco cv SR1 plants. Both progenies of infected plants showed higher levels of somatic HRF, higher resistance to TMV infection and tolerance to methyl methane sulfonate (MMS), an increase in callose deposition, as well as a higher steady-state PATHOGENESIS-RELATED GENE1 (PR1) RNA level compared with the progeny of uninfected plants. Analysis of methylation patterns has revealed global genome hypermethylation in both progenies paralleled by hypomethylation in euchromatic areas.     

Purification, cDNA cloning and homology modeling of endo-1,3-beta-D-glucanase from scallop Mizuhopecten yessoensis

The retaining endo-1,3-β-d-glucanase (LV) with molecular mass of 36 kDa was purified to homogeneity from the crystalline styles of scallop Mizuhopecten yessoensis. The purified enzyme catalyzed hydrolysis of laminaran as endo-enzyme forming glucose, laminaribiose and higher oligosaccharides as products (K_m  600 μg/mL). The 1,3-β-d-glucanase effectively catalyzed transglycosylation reaction that is typical of endo-enzymes too. Optima of pH and temperature were at 4.5 and 45 °C, respectively. cDNA encoding the endo-1,3-β-d-glucanase was cloned by PCR-based methods. It contained an open reading frame that encoded 339-amino acids protein. The predicted endo-1,3-β-d-glucanase amino acid sequence included a characteristic domain of the glycosyl hydrolases family 16 and revealed closest homology with 1,3-β-d-glucanases from bivalve Pseudocardium sachalinensis, sea urchin Strongylocentrotus purpuratus and invertebrates lipopolysaccharide and β-1,3-glucan-binding proteins.The fold of the LV was more closely related to κ-carrageenase, agarase and 1,3;1,4-β-d-glucanase from glycosyl hydrolases family 16. Homology model of the endo-1,3-β-d-glucanase from M. yessoensis was obtained with MOE on the base of the crystal structure of κ-carrageenase from P. carrageonovora as template. Putative three-dimensional structures of the LV complexes with substrate laminarihexaose or glucanase inhibitor halistanol sulfate showed that the binding sites of the halistanol sulfate and laminarihexaose are located in the enzyme catalytic site and overlapped.