Genomic and Epigenomic Mechanisms of the Interaction between Parasitic and Host Plants.

Parasitic plants extract nutrients from the other plants to finish their life cycle and reproduce. The control of parasitic weeds is notoriously difficult due to their tight physical association and their close biological relationship to their hosts. Parasitic plants differ in their susceptible host ranges, and the host species differ in their susceptibility to parasitic plants.

Elongating Effect of the Peptide AEDL on the Root of under Salinity.

The overall survival of a plant depends on the development, growth, and functioning of the roots. Root development and growth are not only genetically programmed but are constantly influenced by environmental factors, with the roots adapting to such changes. The peptide AEDL (alanine-glutamine acid-asparagine acid-leucine) at a concentration of 10 M had an elongating effect on the root cells of seedlings.

Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses.

Unlike animals, plants are immobile and could not actively escape the effects of aggressive environmental factors, such as pathogenic microorganisms, insect pests, parasitic plants, extreme temperatures, drought, and many others. To counteract these unfavorable encounters, plants have evolved very high phenotypic plasticity. In a rapidly changing environment, adaptive phenotypic changes often occur in time frames that are too short for the natural selection of adaptive mutations.

The Effects of Parabiosis on Aging and Age-Related Diseases.

Parabiosis refers to the union of two living organisms by surgical operation, leading to the development of a shared circulatory system. It enables researchers to ask whether or not transmissible factors in the blood of one parabiont have physiological effects on its partner. In other words, parabiosis allows researchers to explore whether circulating factors in the bloodstream can alter tissue function.

Quantitative Analysis of DNA Methylation by Bisulfite Sequencing.

Changes in deoxyribonucleic acid (DNA) methylation are shown to occur with aging in mammals. Besides changes that seem to be essentially stochastic, methylation levels of certain CpG sites display a strong correlation with age. Collectively, methylation of such CpG sites could be used as "epigenetic clocks" to predict biological age.

Epigenetic Clock: Just a Convenient Marker or an Active Driver of Aging?

A global DNA hypomethylation and local changes in the methylation levels of specific DNA loci occur during aging in mammals. Global hypomethylation mainly affects highly methylated repeat sequences, such as transposable elements; it is an essentially stochastic process usually referred to as "epigenetic drift." Specific changes in DNA methylation affect various genome sequences and could be either hypomethylation or hypermethylation, but the prevailing tendencies are hypermethylation of promoter sequences associated with CpG islands and hypomethylation of CpG poor genes.

Epigenetic Regulation of Plant Gametophyte Development.

Unlike in animals, the reproductive lineage cells in plants differentiate from within somatic tissues late in development to produce a specific haploid generation of the life cycle-male and female gametophytes. In flowering plants, the male gametophyte develops within the anthers and the female gametophyte-within the ovule. Both gametophytes consist of only a few cells.

Aging as an Epigenetic Phenomenon.

Introduction: Hypermethylation of genes associated with promoter CpG islands, and hypomethylation of CpG poor genes, repeat sequences, transposable elements and intergenic genome sections occur during aging in mammals. Methylation levels of certain CpG sites display strict correlation to age and could be used as "epigenetic clock" to predict biological age. Multi-substrate deacetylases SIRT1 and SIRT6 affect aging via locus-specific modulations of chromatin structure and activity of multiple regulatory proteins involved in aging.

Short Exogenous Peptides Regulate Expression of CLE, KNOX1, and GRF Family Genes in Nicotiana tabacum.

Exogenous short biologically active peptides epitalon (Ala-Glu-Asp-Gly), bronchogen (Ala-Glu-Asp-Leu), and vilon (Lys-Glu) at concentrations 10-10 M significantly influence growth, development, and differentiation of tobacco (Nicotiana tabacum) callus cultures. Epitalon and bronchogen, in particular, both increase growth of calluses and stimulate formation and growth of leaves in plant regenerants. Because the regulatory activity of the short peptides appears at low peptide concentrations, their action to some extent is like that of the activity of phytohormones, and it seems to have signaling character and epigenetic nature.

Regulatory Peptides in Plants.

Many different peptides regulating cell differentiation, growth, and development are found in plants. Peptides participate in regulation of plant ontogenesis starting from pollination, pollen tube growth, and the very early stages of embryogenesis, including formation of embryo and endosperm. They direct differentiation of meristematic stem cells, formation of tissues and individual organs, take part in regulation of aging, fruit maturation, and abscission of plant parts associated with apoptosis.

[Dnmt2 is the Most Evolutionary Conserved and Enigmatic Cytosine DNA Methyltransferase in Eukaryotes].

Dnmt2 is the most strongly conserved cytosine DNA methyltransferase in eukaryotes. It has been found in all organisms possessing methyltransferases of the Dnmt1 and Dnmt3 families, whereas in many others Dnmt2 is the sole cytosine DNA methyltransferase. The Dnmt2 molecule contains all conserved motifs of cytosine DNA methyltransferases.

Plant DNA Methyltransferase Genes: Multiplicity, Expression, Methylation Patterns.

Expression and methylation patterns of genes encoding DNA methyltransferases and their functionally related proteins were studied in organs of Arabidopsis thaliana plants. Genes coding for the major maintenance-type DNA methyltransferases, MET1 and CMT3, and the major de novo-type DNA methyltransferase, DRM2, are actively expressed in all organs. Similar constitutively active expression was observed for genes encoding their functionally related proteins, a histone H3K9 methyltransferase KYP and a catalytically non-active protein DRM3.

Aging Epigenetics: Accumulation of Errors or Realization of a Specific Program?

Aging in mammals is known to be accompanied by a progressive loss of methylated cytosines from DNA. This loss is tissue-specific to a certain extent and affects mainly repeated sequences, transposable elements, and intergenic genome parts. Age-dependent DNA hypomethylation is correlated with and perhaps partly caused by a diminished activity of DNA methyltransferases.

[Epigenetic mutagenesis as program of age-related protein dysfunction and aging].

DNA methylation plays an important polyfunctional role in ontogenesis of human and mammals. A steep rise in probability of mutational substitution of CpG dinucleotide on TpG dinucleotide in the genome is one of the consequences of DNA methylation. All spectrum (17) of possible DNA and protein mutations caused by CpG-dinucleotide methylation in DNA were characterized, and the three most dangerous mutations (able to result in protein inactivation) were isolated.

Epigenetic mechanisms of peptidergic regulation of gene expression during aging of human cells.

Expression levels of genes encoding specific transcription factors and other functionally important proteins vary upon aging of pancreatic and bronchial epithelium cell cultures. The peptides KEDW and AEDL tissue-specifically affect gene expression in pancreatic and bronchial cell cultures, respectively. It is established in this work that the DNA methylation patterns of the PDX1, PAX6, NGN3, NKX2-1, and SCGB1A1 gene promoter regions change upon aging in pancreatic and bronchial cell cultures in correlation with variations in their expression levels.

Peptide regulation of gene expression and protein synthesis in bronchial epithelium.

Introduction: Some studies have shown that peptides have high treatment potential due to their biological activity, harmlessness, and tissue-specific action. Tetrapeptide Ala-Asp-Glu-Leu (ADEL) was effective on models of acute bacterial lung inflammation, fibrosis, and toxic lung damage in several studies.

Methods: We measured Ki67, Mcl-1, p53, CD79, and NOS-3 protein levels in the 1st, 7th, and 14th passages of bronchoepithelial human embryonic cell cultures.

Modulation of action of wheat seedling endonucleases WEN1 and WEN2 by histones.

Wheat core histones and various subfractions of histone H1 modulate differently the action of endonucleases WEN1 and WEN2 from wheat seedlings. The character of this modulation depends on the nature of the histone and the methylation status of the substrate DNA. The modulation of enzyme action occurs at different stages of processive DNA hydrolysis and is accompanied by changes in the site specificity of the enzyme action.

Interaction of short peptides with FITC-labeled wheat histones and their complexes with deoxyribooligonucleotides.

Judging from fluorescence modulation (quenching), short peptides (Ala-Glu-Asp-Gly, Glu-Asp-Arg, Ala-Glu-Asp-Leu, Lys-Glu-Asp-Gly, Ala-Glu-Asp-Arg, and Lys-Glu-Asp-Trp) bind with FITC-labeled wheat histones H1, H2B, H3, and H4. This results from the interaction of the peptides with the N-terminal histone regions that contain respective and seemingly homologous peptide-binding motifs. Because homologous amino acid sequences in wheat core histones were not found, the peptides seem to bind with some core histone regions having specific conformational structure.

Mechanisms of catalytic action and chemical modifications of endonucleases WEN1 and WEN2 from wheat seedlings.

Hydrolysis of DNA catalyzed by wheat endonucleases WEN1 and WEN2 is pronouncedly processive. A correlation has been revealed between appearance of new products of DNA hydrolysis with different length and conformational changes in the enzymes. The first conformational conversion of the endonucleases is associated with appearance of large fragments of DNA hydrolysis with length longer than 500 bp, and the second conversion is associated with formation of oligonucleotides with length of 120-140 bp, and the third conversion is associated with formation of short oligonucleotides and mononucleotides.

Endonucleases and apoptosis in animals.

Endonucleases are the main instruments of obligatory DNA degradation in apoptosis. Many endonucleases have marked processive action; initially they split DNA in chromatin into very large domains, and then they perform in it internucleosomal fragmentation of DNA followed by its hydrolysis to small fragments (oligonucleotides). During apoptosis, DNA of chromatin is attacked by many nucleases that are different in activity, specificity, and order of action.

Processing character of the action of wheat endonucleases WEN1 and WEN2. Kinetic parameters.

The wheat seedling endonucleases WEN1 and WEN2 dependent on Mg(2+), Ca(2+), and S-adenosyl-L-methionine (SAM) and sensitive to the substrate DNA methylation status have an expressed processing action. The enzymes hydrolyze DNA at a few subsequent stages: first, they split λ phage DNA specifically at CNG-sites (WEN1) with liberation of large fragments; second, they hydrolyze these fragments to 120-140 bp oligonucleotides that finally are hydrolyzed to very short fragments and mononucleotides. Initial stages of DNA hydrolysis may proceed in the absence of Mg(2+), but subsequent hydrolysis stages are very strongly stimulated by Mg(2+).

Role of peptides in epigenetic regulation of gene activities in ontogeny.

The authors develop a new concept most fully reflecting the evolutional and biological role of peptides in the organism. Wide spectrum of peptide effects realized through regulation of the expression of certain genes is aimed at the maintenance of homeostasis, inhibition of the genetic aging program realization, and lifespan prolongation.

Site-specific binding of short peptides with DNA modulated eukaryotic endonuclease activity.

Short peptides (2-4 amino acid residues) inhibit or stimulate hydrolysis of λ phage DNA by eukaryotic endonucleases WEN1 and WEN2 depending on DNA methylation status. Peptide modulation of endonucleases activity most likely appears as a result of their binding to DNA. Peptides discriminate (recognize) not only certain DNA sequences, but also their methylation status.

Penetration of short fluorescence-labeled peptides into the nucleus in HeLa cells and in vitro specific interaction of the peptides with deoxyribooligonucleotides and DNA.

Marked fluorescence in cytoplasm, nucleus, and nucleolus was observed in HeLa cells after incubation with each of several fluorescein isothiocyanate-labeled peptides (epithalon, Ala-Glu-Asp-Gly; pinealon, Glu-Asp-Arg; testagen, Lys-Glu-Asp-Gly). This means that short biologically active peptides are able to penetrate into an animal cell and its nucleus and, in principle they may interact with various components of cytoplasm and nucleus including DNA and RNA. It was established that various initial (intact) peptides differently affect the fluorescence of the 5,6-carboxyfluorescein-labeled deoxyribooligonucleotides and DNA-ethidium bromide complexes.