Laser microdissection of pisum sativum l. Nodules followed by rna‐seq analysis revealed crucial transcriptomic changes during infected cell differentiation

Garden pea (Pisum sativum L.) is a globally important legume crop. Like other legumes, it forms beneficial symbiotic interactions with the soil bacteria rhizobia, gaining the ability to fix at-mospheric nitrogen. In pea nodules, the meristem is long‐lasting and results in the formation of several histological zones that implicate a notable differentiation of infected host cells. However, the fine transcriptional changes that accompany differentiation are still unknown. In this study, using laser microdissection followed by RNA‐seq analysis, we performed transcriptomic profiling in the early infection zone, late infection zone, and nitrogen fixation zone of 11‐day‐old nodules of pea wild‐type line SGE. As a result, a list of functional groups of differentially expressed genes (DEGs) in different nodule histological zones and a list of genes with the most prominent expression changes during nodule development were obtained. Their analyses demonstrated that the highest amount of DEGs was associated with the nitrogen fixation zone. Among well‐known genes controlling nodule development, we revealed genes that can be novel players throughout nodule for-mation. The characterized genes in pea were compared with those previously described in other legumes and their possible functions in nodule development are discussed

Transcriptomic data of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S treated with novobiocin

© 2020 The Authors In enteric bacteria, DNA supercoiling is highly responsive to environmental conditions. Host specific features of environment serve as cues for the expression of genes required for colonization of host niches via changing supercoiling [1]. It has been shown that substitution at position 87 of GyrA of Salmonella enterica str. SL1344 influences global supercoiling and results in an altered transcriptome with increased expression of stress response pathways [2]. Aminocoumarin antibiotics, such as novobiocin, can be used to relax supercoiling and alter the expression of supercoiling-sensitive genes. Meanwhile, Salmonella enterica demonstrates a significant resistance to this antibiotic and relatively small variability of supercoiling in response to the growth phase, osmotic pressure, and novobiocin treatment. Here we present for the first time transcriptome data of Salmonella enterica subsp. Enterica serovar Typhimurium str. 14028S grown in the presence of novobiocin. These data will help identify genes involved in novobiocin resistance and adaptation processes associated with torsion perturbations in S. enterica. Cleaned FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA, Identifier: SRP239815) and have been assigned BioProject accession PRJNA599397

Dataset for transcriptome analysis of abscisic acid degrading bacterium Novosphingobium sp. P6W

© 2019 The Author(s) Plant growth-promoting rhizobacteria (PGPR) improve plant productivity and stress resistance. The mechanisms involved in plant-microbe interactions include the modulation of plant hormone status. The Novosphingobium sp. strain P6W was previously described as the bacterium capable of abscisic acid (ABA) degradation, and its inoculation decreased ABA concentrations in planta. The metabolic pathway for the ABA degradation in bacteria is still unknown. Here we present transcriptome data of Novosphingobium sp. P6W grown in the medium supplemented with ABA or fructose as the carbon source. Cleaned FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA, Identifier: SRP189498) and have been assigned BioProject accession PRJNA529223

Dataset for transcriptome analysis of Salmonella enterica subsp. enterica serovar Typhimurium strain 14028S response to starvation

© 2020 The Author(s) Salmonella enterica is an ubiquitous pathogen throughout the world causing gastroenteritis in humans and animals. Survival of pathogenic bacteria in the external environment may be associated with the ability to overcome the stress caused by starvation. The bacterial response to starvation is well understood in laboratory cultures with a sufficiently high cell density. However, bacterial populations often have a small size when facing this challenge in natural biotopes. The aim of this work was to find out if there are differences in the transcriptomes of S. enterica depending on the factor of cell density during starvation. Here we present transcriptome data of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S grown in carbon rich or carbon deficient medium with high or low cell density. These data will help identify genes involved in adaptation of low-density bacterial populations to starvation conditions

Pillar[5]arenes as potential personage for DNA compactization and gene therapy

© 2020 Elsevier B.V. Here we demonstrated that pillar[5]arenes with counterions I− and Cl− show the ability to plasmid compactization and increasing bacterial transformation efficiently. Pillar[5]arenes have been tested for binding with palindromic decamer oligonucleotide and interacting with plasmid DNA. The complexation of pillar[5]arene with oligonucleotide has been shown by NMR- and CD-spectroscopy. Pillar[5]arenes form complexes with oligonucleotide in solution in the 1:1 or 1:2 stoichiometry. Molecular modeling allowed to constructs the models of these complexes. Pillar[5]arene interaction with the plasmid DNA have been studied using atomic force microscopy. According to AFM images pillar[5]arene-I− and pillar[5]arene-Cl− packed up the plasmid DNA to aggregates with diameter about 100 nm with different morphology. An increase in DNA transformation efficiency into bacterial cells has been shown for pillar[5]arenes with counterions I− and Cl−

Comparative Study of the Abscisic Acid Metabolism Using Analogue Tritium-Labeled in the Cyclohexene or Side Moiety

© 2020, Pleiades Publishing, Ltd. Abstract: A procedure was developed for introducing tritium into the side chain of the abscisic acid (ABA) molecule. The reaction was carried out in dioxane in the presence of the Lindlar catalyst. The yield of the labeled product was 70% and the molar radioactivity was 44 Ci/mol. The tritium-labeled abscisic acid analogue was found to be a growth substrate for soil bacteria that incorporate a radioactive label into cellular metabolites. The absorption of the label by bacteria from the side chain of abscisic acid is more than an order of magnitude higher than that for labeling in the cyclohexene moiety. The results indicate the existence of a previously unknown metabolism pathway of ABA in microorganisms

Metabolism by Rhizobacteria of Abscisic Acid Deuterated in the Cyclohexene Part

The required amount of abscisic acid containing 4 – 5 D atoms ([2H]ABA) in the cyclohexene fragment of the molecule was produced via isotope exchange in 100% deuterated D2O at 220°C in the presence of diisopropyl ethylamine. The yield of labeled compound was 45 – 80%. A complex of biological studies was carried out using the D-labeled preparation. It was established that [2H]ABAserved as a growth substrate for soil bacteria, which included the isotopic label in the composition of cell metabolites. The characteristics of D-labeled metabolites allowed their reliable identification in mass spectra of the total bacterial metabolome. Three intermediates of a new metabolic pathway of microbial degradation of this phytohormone were identified using the developed technique

Rhizosphere bacterium rhodococcus sp. P1y metabolizes ab-scisic acid to form dehydrovomifoliol

The phytohormone abscisic acid (ABA) plays an important role in plant growth and in response to abiotic stress factors. At the same time, its accumulation in soil can negatively affect seed germination, inhibit root growth and increase plant sensitivity to pathogens. ABA is an inert compound resistant to spontaneous hydrolysis and its biological transformation is scarcely under-stood. Recently, the strain Rhodococcus sp. P1Y was described as a rhizosphere bacterium assimilat-ing ABA as a sole carbon source in batch culture and affecting ABA concentrations in plant roots. In this work, the intermediate product of ABA decomposition by this bacterium was isolated and purified by preparative HPLC techniques. Proof that this compound belongs to ABA derivatives was carried out by measuring the molar radioactivity of the conversion products of this phytohor-mone labeled with tritium. The chemical structure of this compound was determined by instrumen-tal techniques including high-resolution mass spectrometry, NMR spectrometry, FTIR and UV spec-troscopies. As a result, the metabolite was identified as (4RS)-4-hydroxy-3,5,5-trimethyl-4-[(E)-3-oxobut-1-enyl]cyclohex-2-en-1-one (dehydrovomifoliol). Based on the data obtained, it was con-cluded that the pathway of bacterial degradation and assimilation of ABA begins with a gradual shortening of the acyl part of the molecule