Genomic and Transcriptomic Analysis of Pea ( L.) Breeding Line 'Triumph' with High Symbiotic Responsivity.

Pea ( L.), like most legumes, forms mutualistic symbioses with nodule bacteria and arbuscular mycorrhizal (AM) fungi. The positive effect of inoculation is partially determined by the plant genotype; thus, pea varieties with high and low symbiotic responsivity have been described, but the molecular genetic basis of this trait remains unknown.

Identification and Expression Analysis of the Family in L.

The (CEP) peptides play crucial roles in plant growth and response to environmental factors. These peptides were characterized as positive regulators of symbiotic nodule development in legume plants. However, little is known about the CEP peptide family in pea.

A variable gene family encoding nodule-specific cysteine-rich peptides in pea ( L.).

Various legume plants form root nodules in which symbiotic bacteria (rhizobia) fix atmospheric nitrogen after differentiation into a symbiotic form named bacteroids. In some legume species, bacteroid differentiation is promoted by defensin-like nodule-specific cysteine-rich (NCR) peptides. NCR peptides have best been studied in the model legume Gaertn.

The Regulation of Pea ( L.) Symbiotic Nodule Infection and Defense Responses by Glutathione, Homoglutathione, and Their Ratio.

In this study, the roles of glutathione (GSH), homoglutathione (hGSH), and their ratio in symbiotic nodule development and functioning, as well as in defense responses accompanying ineffective nodulation in pea () were investigated. The expression of genes involved in (h)GSH biosynthesis, thiol content, and localization of the reduced form of GSH were analyzed in nodules of wild-type pea plants and mutants (weak allele, "locked" infection threads, occasional bacterial release, and defense reactions) and (strong allele, "locked" infection threads, defense reactions), and (abnormal bacteroids, oxidative stress, early senescence, and defense reactions). The effects of (h)GSH depletion and GSH treatment on nodule number and development were also examined.

A high coverage reference transcriptome assembly of pea (Pisum sativum L.) mycorrhizal roots.

Arbuscular mycorrhiza (AM) is an ancient mutualistic symbiosis formed by 80-90 % of land plant species with the obligatorily biotrophic fungi that belong to the phylum Glomeromycota. This symbiosis is mutually beneficial, as AM fungi feed on plant photosynthesis products, in turn improving the efficiency of nutrient uptake from the environment. The garden pea (Pisum sativum L.

Efficacy of a Plant-Microbe System: (L.) Cadmium-Tolerant Mutant and Strains, Expressing Pea Metallothionein Genes and , for Cadmium Phytoremediation.

Two transgenic strains of bv. , 3841-PsMT1 and 3841-PsMT2, were obtained. These strains contain the genetic constructions and coding for two pea ( L.

[Opposite Effects of Histone H1 and HMGN5 Protein on Distant Interactions in Chromatin].

Transcriptional enhancers in the cell nuclei typically interact with the target promoters over long stretches of chromatin, but the mechanism of this communication remains unknown. Previously we have developed a defined system for quantitative analysis of the rate of distant enhancer-promoter communication (EPC) and have shown that the chromatin fibers maintain efficient distant EPC . Here we investigate the roles of linker histone H1 and HMGN5 protein in EPC.

New sources of allele in the pea ( L.) carry the unique variant of candidate LysM-RLK gene .

At the onset of legume-rhizobial symbiosis, the mutual recognition of partners occurs based on a complicated interaction between signal molecules and receptors. Bacterial signal molecules named Nod factors ("nodulation factors") are perceived by the plant LysM-containing receptor-like kinases (LysM-RLKs) that recognize details of its structure (i.e.

Mapping-by-sequencing using NGS-based 3'-MACE-Seq reveals a new mutant allele of the essential nodulation gene () in pea ( L.).

Large collections of pea symbiotic mutants were accumulated in the 1990s, but the causal genes for a large portion of the mutations are still not identified due to the complexity of the task. We applied a Mapping-by-Sequencing approach including Bulk Segregant Analysis and Massive Analysis of cDNA Ends (MACE-Seq) sequencing technology for genetic mapping the gene of pea which controls the formation of symbioses with both nodule bacteria and arbuscular-mycorrhizal fungi. For mapping we developed an -population from the cross between pea line N24 carrying the mutant allele of and the wild type NGB1238 (=JI0073) line.

Mechanism of FACT removal from transcribed genes by anticancer drugs curaxins.

Human FACT (facilitates chromatin transcription) is a multifunctional protein complex that has histone chaperone activity and facilitates nucleosome survival and transcription through chromatin. Anticancer drugs curaxins induce FACT trapping on chromatin of cancer cells (c-trapping), but the mechanism of c-trapping is not fully understood. Here, we show that in cancer cells, FACT is highly enriched within the bodies of actively transcribed genes.

Pea Marker Database (PMD) - A new online database combining known pea (Pisum sativum L.) gene-based markers.

Pea (Pisum sativum L.) is the oldest model object of plant genetics and one of the most agriculturally important legumes in the world. Since the pea genome has not been sequenced yet, identification of genes responsible for mutant phenotypes or desirable agricultural traits is usually performed via genetic mapping followed by candidate gene search.

Nucleosome-free DNA regions differentially affect distant communication in chromatin.

Communication between distantly spaced genomic regions is one of the key features of gene regulation in eukaryotes. Chromatin per se can stimulate efficient enhancer-promoter communication (EPC); however, the role of chromatin structure and dynamics in this process remains poorly understood. Here we show that nucleosome spacing and the presence of nucleosome-free DNA regions can modulate chromatin structure/dynamics and, in turn, affect the rate of EPC in vitro and in silico.

Overcoming a nucleosomal barrier to replication.

Efficient overcoming and accurate maintenance of chromatin structure and associated histone marks during DNA replication are essential for normal functioning of the daughter cells. However, the molecular mechanisms of replication through chromatin are unknown. We have studied traversal of uniquely positioned mononucleosomes by T7 replisome in vitro.

Large-scale ATP-independent nucleosome unfolding by a histone chaperone.

DNA accessibility to regulatory proteins is substantially influenced by nucleosome structure and dynamics. The facilitates chromatin transcription (FACT) complex increases the accessibility of nucleosomal DNA, but the mechanism and extent of its nucleosome reorganization activity are unknown. Here we determined the effects of FACT from the yeast Saccharomyces cerevisiae on single nucleosomes by using single-particle Förster resonance energy transfer (spFRET) microscopy.

Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription.

RNA polymerase II (Pol II) transcription through chromatin is accompanied by formation of small intranucleosomal DNA loops. Pol II captured within a small loop drives accumulation of DNA supercoiling, facilitating further transcription. DNA breaks relieve supercoiling and induce Pol II arrest, allowing detection of DNA damage hidden in chromatin structure.

[Structure and function of histone chaperone FACT].

FACT is heterodimer protein complex and histone chaperone that plays an important role in maintaining and modifying chromatin structure during various DNA-dependent processes. FACT is involved in nucleosome assembly de novo and in the preservation and recovery of the nucleosome structure during and after transcription, replication and repair of DNA. During transcript elongation FACT reduces the height of the nucleosome barrier and supports survival of the nucleosomes during and after passage of RNA polymerase II.

De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome.

The large size and complexity of the garden pea (Pisum sativum L.) genome hamper its sequencing and the discovery of pea gene resources. Although transcriptome sequencing provides extensive information about expressed genes, some tissue-specific transcripts can only be identified from particular organs under appropriate conditions.

Structure of transcribed chromatin is a sensor of DNA damage.

Early detection and repair of damaged DNA is essential for cell functioning and survival. Although multiple cellular systems are involved in the repair of single-strand DNA breaks (SSBs), it remains unknown how SSBs present in the nontemplate strand (NT-SSBs) of DNA organized in chromatin are detected. The effect of NT-SSBs on transcription through chromatin by RNA polymerase II was studied.

PARP1 Inhibitors: antitumor drug design.

The poly (ADP-ribose) polymerase 1 (PARP1) enzyme is one of the promising molecular targets for the discovery of antitumor drugs. PARP1 is a common nuclear protein (1-2 million molecules per cell) serving as a "sensor" for DNA strand breaks. Increased PARP1 expression is sometimes observed in melanomas, breast cancer, lung cancer, and other neoplastic diseases.

[Molecular mechanisms of regulaion of transcription by PARP1].

Poly-ADP-ribosylation is a covalent post-translational modification of nuclear proteins that plays a key role in the immediate response of cells to genotoxic stress. Poly(ADP-ribose) polymerase (PARP) synthesizes long and branched polymers of ADP-ribose onto acceptor regulator proteins, and thereby change their activity. Metabolism of poly-ADP regulates DNA repair, cell cycle, replication, aging and death of cells, as well as remodeling of chromatin structure and gene transcription.

Preparation of mononucleosomal templates for analysis of transcription with RNA polymerase using spFRET.

Single positioned nucleosomes have been extensively employed as simple model experimental systems for analysis of various intranuclear processes. Here we describe an experimental system containing positioned mononucleosomes allowing transcription by various RNA polymerases. Each DNA template contains a pair of fluorescent labels (Cy3 and Cy5) allowing measuring relative distances between the neighboring coils of nucleosomal DNA using Forster resonance energy transfer (FRET).

Preparation and analysis of positioned mononucleosomes.

Short DNA fragments containing single nucleosomes have been extensively employed as simple model experimental systems for analysis of many intranuclear processes, including binding of proteins to nucleosomes, covalent histone modifications, transcription, DNA repair, and ATP-dependent chromatin remodeling. Here we describe several recently developed procedures for obtaining and analysis of mononucleosomes assembled on 200-350-bp DNA fragments.

Experimental analysis of hFACT action during Pol II transcription in vitro.

FACT (facilitates chromatin transcription) is a histone chaperone that facilitates transcription through chromatin and promotes histone recovery during transcription. Here, we describe a highly purified experimental system that recapitulates many important properties of transcribed chromatin and the key aspects of hFACT action during this process in vitro. We present the protocols describing how to prepare different forms of nucleosomes, including intact nucleosome, covalently conjugated nucleosome, nucleosome missing one of the two H2A/2B dimers (hexasome) and tetrasome (a nucleosome missing both H2A/2B dimers).