Yuri Gogolev

• Russian Academy of Sciences

Mapping transcription start sites and determining their activity remain a challenging task even for well-studied organisms. Here, we present Cappable-seq RNA sequencing data of Escherichia coli K-12 MG1655 after treatment with three antibiotics with various spectra of action that may expand the range of mapped transcription start sites for this mod...

Being facultative intracellular pathogens, the bacterium often is found in the environment. In natural habitats Salmonella are able to survive and multiply inside free-living protists that support preservation and distribution of the pathogen, its virulence and resistance to antimicrobial agents. At the same time, the expression profile of Salmonel...

The alternative sigma factor RpoS is considered to be one of the major regulators providing stress resistance and cross-protection in bacteria. In phytopathogenic bacteria, the effects of RpoS have not been analyzed with regard to cross-protection, and genes whose expression is directly or indirectly controlled by RpoS have not been determined at t...

Background Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Sout...

The Shulgan-Tash (Kapova) cave is a unique object for scientific research. In this article, we report the draft genome sequence of Janibacter limosus strain P1(28)-3 (RCAM05316) isolated from cave lime mud, Russia (53° 2′ 0″ N, 57° 3′ 0″ E). The sequence was obtained using Oxford Nanopore Technologies MinION.

Bacterial adaptation is regulated at the population level with the involvement of intercellular communication (quorum sensing). When the population density is insufficient for adaptation under starvation, bacteria can adjust it to a quorum level through cell divisions at the expense of endogenous resources. This phenomenon has been described for th...

In this article, we report the complete genome sequences of Massilia sp. strains B-10 (RCAM05335) and H-1 (RCAM05339), which were isolated from the water of the Dal’nee Verkhnee Lake in the Shulgan-Tash cave in Russia (53°2′0″N, 57°3′0″E). The sequences were obtained using an Oxford Nanopore Technologies MinION system.

Pink snow mold, caused by a phytopathogenic and psychrotolerant fungus, Microdochium nivale, is a severe disease of winter cereals and grasses that predominantly occurs under snow cover or shortly after its melt. Snow mold has significantly progressed during the past decade, often reaching epiphytotic levels in northern countries and resulting in d...

The Shulgan-Tash cave is an extremely interesting object for scientific research, located in the Republic of Bashkortostan (Russia). In this article, we report the complete genome sequence of Rhizobium sp. strain RCAM05350 isolated from the “cave silver” biofilms. The sequence was obtained using Oxford Nanopore Technologies MinION.

Background: Laboratory experiments with starving cultures indicate that a wide range of microorganisms show genetic traits that improve stability for oligotrophic conditions. However, it remains unclear to what extent laboratory studies of starvation survival in pure or mixed cultures can be extrapolated to stable microbial ecosystems in nature. Mo...

Microdochium nivale is a progressive and devastating phytopathogen that causes different types of cereal crop and grass diseases that are poorly characterized at the molecular level. Although rye (Secale cereale L.) is one of the most resistant crops to most of the phytopathogens, it is severely damaged by M. nivale. The recent high-quality chromos...

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 atmospheric nitrogen. In pea nodules, the meristem is long-lasting and results in the formation of several histological zones that implicate a notable different...

The phytopathogenic bacterium Pectobacterium atrosepticum (Pba), one of the members of the soft rot Pectobacteriaceae, forms biofilm-like structures known as bacterial emboli when colonizing the primary xylem vessels of the host plants. The initial extracellular matrix of the bacterial emboli is composed of the host plant’s pectic polysaccharides,...

Siderophores produced by microorganisms to scavenge iron from the environment have been shown to contribute to virulence and/or stress resistance of some plant pathogenic bacteria. Phytopathogenic bacteria of Pectobacterium genus possess genes for the synthesis of siderophore enterobactin, which role in plant-pathogen interactions has not been eluc...

The bacterial pathogen Salmonella enterica, which causes enteritis, has a broad host range and extensive environmental longevity. In water and soil, Salmonella interacts with protozoa and multiplies inside their phagosomes. Although this relationship resembles that between Salmonella and mammalian phagocytes, the interaction mechanisms and bacteria...

Background and Aims Plant diseases caused by Pectobacterium atrosepticum are often accompanied by extensive rot symptoms. In addition, these bacteria are able to interact with host plants without causing disease for long periods, even throughout several host plant generations. There is, to date, no information on the comparative physiology/biochemi...

Stringent response (SR), a primary stress reaction in bacteria and plant chloroplasts, is a molecular switch that provides operational stress-induced reprogramming of transcription under conditions of abiotic and biotic stress. Given that the infection is a stressful situation for both partners, the host plant and the pathogen, we analyzed the expr...

The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require mu...

Our study is the first to consider the changes in the entire set of matrix plant cell wall (PCW) polysaccharides in the course of a plant infectious disease. We compared the molecular weight distribution, monosaccharide content, and the epitope distribution of pectic compounds and cross-linking glycans in non-infected potato plants and plants infec...

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 tr...

Pectobacterium versatile (formerly P. carotovorum) is a recently defined species of soft rot enterobacteria capable of infecting many plant hosts and damaging different tissues. Complex transcriptional regulation of virulence properties can be expected for such a versatile pathogen. However, the relevant information is available only for related sp...

Rhizosphere bacteria are capable of utilizing various phytohormones (particularly auxins) as nutrients and thereby affect plant growth, nutrition and interactions with symbiotic microorganisms. Here, for the first time we evaluated the effects of rhizosphere bacteria Novosphingobium sp. P6W and Rhodococcus sp. P1Y capable of utilizing abscisic acid...

A comparative analysis of transcriptomes at the vegetative and generative stages of the development of Lentinus edodes basidiomycetes was carried out. The nature of differential gene expression was described, and the activated/repressed metabolic pathways were visualized.

We propose an algorithm for RNA-Seq data analysis useful for revealing the “master regulators” of gene expression in experimental condition, as well as of cis-elements regulating transcript level of genes from certain groups.

The intensity of root colonization by phytopathogenic fungus and rhizobacterium differs depending on the tomato genotype. Inoculation of wild-type tomatoes Ailsa Craig, but not of its ABA deficient mutant flacca, with Novosphingobium sp. P6W inhibits root colonization by Fusarium oxysporum MF-G284.

Using laser capture microdissection, a comparative analysis of transcriptomes of three histological zones of pea nodules was performed.

Phytopathogenic pectobacteria produce extracellular low-molecular-weight phosphonates which possibly determine the strategy for the plant-microbe interaction.

We performed a genomic analysis of the presence and organization of oxygenases involved in the hydroxylation of various substrates, including the aromatic ring, and dioxygenases catalyzing a ring-cleavage of the formed hydroxylated intermediates in A. brasilense SR80.

There are “molecular switchers” that transform peaceful coexistence of plants with phytopathogenic pectobacteria to symptomatic infection. These switchers seem to be perspective “targets” for plant protection approaches.

Snow mold is a severe plant disease caused by psychrophilic or psychrotolerant fungi, of which Microdochium species are the most harmful. A clear understanding of Microdochium biology has many gaps; the pathocomplex and its dynamic are poorly characterized, virulence factors are unknown, genome sequences are not available, and the criteria of plant...

Soft rot caused by Pectobacterium species is a devastating plant disease poorly characterized in terms of host plant responses. In this study, changes in the transcriptome of tobacco plants after infection with Pectobacterium atrosepticum (Pba) were analyzed using RNA-Seq. To draw a comprehensive and nontrivially itemized picture of physiological e...

RNA-Seq transcriptome data for the wild type and phoP mutant strains of Pectobacterium versatile is described. P. versatile is a recently introduced name for a species of plant pathogenic bacteria that unites a group of strains previously embedded within the Pectobacterium carotovorum clade [1,2]. Little detail is available about how this pathogen...

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...

A collection of rhizobial strains isolated from root nodules of the narrowly endemic legume species Oxytropis erecta, O. anadyrensis, O. kamtschatica and O. pumilio originated from the Kamchatka Peninsula (Russian Federation) was obtained. Analysis of the 16S rRNA gene sequence showed a significant diversity of isolates belonging to families Rhizob...

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 sufficient...

The PhoPQ two-component system, originally described in pectobacteria as PehRS, was previously shown to regulate a single gene, pehA. Using an insertional phoP mutant of Pectobacterium versatile, we demonstrate that PhoP controls a regulon of at least 116 genes with a large fraction of regulon members specific for pectobacteria. The functions perfo...

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 globa...

In our study, the rare earth element ytterbium (Yb³⁺) was demonstrated to affect water exchange in roots of Zea mays seedlings. Herewith, the overall membrane permeability (Pd) increased. The Pd increase was determined by aquaporin activity but not the membrane lipid component since the closure of aquaporin channels due to low intracellular pH abol...

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...

Mechanisms of microbial catabolism of phytohormone abscisic acid (ABA) are still unknown. Here, we report the complete genome sequence of ABA-utilizing Rhodococcus sp. strain P1Y, isolated from the rice ( Oryza sativa L.) rhizosphere. The sequence was obtained using an approach combining Oxford Nanopore Technologies MinION and Illumina MiSeq sequen...

The phytohormone abscisic acid (ABA) plays multiple roles in plant survival and fitness. Significant quantities of ABA are constantly introduced into soil via root exudation, root turnover and incorporation of abscised shoot tissues. In addition, some phytopathogenic fungi synthesize ABA in the course of plant–microbe interactions. The accumulation...

Herein, for the first time the complexation ability of a homological series of triphenylphosphonium surfactants (TPPB- n ) toward DNA decamers has been explored.

A procedure for tritiation of predominantly the cyclohexene moiety of abscisic acid was developed. Tritium was introduced by isotope exchange reaction with 100% tritiated water at 220°C in the presence of diisopropylethylamine. The yield of abscisic acid was 50%, and the specific activity was 30.5 Ci/mmol. The labeled product was tested. It was sho...

Modern techniques of next-generation sequencing (NGS) allow obtaining expression profile of all genes and provide an essential basis for characterizing metabolism in the organism of interest on a broad scale. An important condition for obtaining a demonstrative physiological picture using high throughput sequencing data is the availability of the g...

Modern techniques of next-generation sequencing (NGS) allow obtaining expression profile of all genes and provide an essential basis for characterizing metabolism in the organism of interest on a broad scale. An important condition for obtaining a demonstrative physiological picture using high throughput sequencing data is the availability of the g...

In the present study, we have monitored the process of systemic plant colonization by the plant pathogenic bacterium Pectobacterium atrosepticum (Pba) using RNA-Seq analysis in order to compare bacterial traits under in planta and in vitro conditions and to reveal potential players that participate in switching from stealth to brute force strategy...

In the present study, we identified exopolysaccharides of the harmful phytopathogenic bacterium Pectobacterium atrosepticum SCRI1043 and characterized the molecular structure of these polymers. The synthesis of the target polysaccharides was shown to be induced under starvation conditions. Moreover, intensive accumulation of exopolysaccharides occu...

In the present study, we attempted to elucidate if the harmful phytopathogenic bacteria of Pectobacterium genus (P. atrosepticum) possess the enzymes for oxidation of phenolic compounds. Polyphenol oxidase (laccase) activity was revealed in P. atrosepticum cell lysates. Using bioinformatic analysis, an ORF encoding a putative copper-containing poly...

Necrotrophic pectobacteria cause severe parenchymatous rots in plants. Expression of symptoms caused by these bacteria is preceded by latent infection, when pathogen predominantly inhabits xylem vessels, prepares the host for further colonization, and behaves as biotroph. Herewith, the strategy of pathogen behavior is changed from "outside" to "ins...

Functional specialization of cells is among the most fundamental processes of higher organism ontogenesis. The major obstacle to studying this phenomenon in plants is the difficulty of isolating certain types of cells at defined stages of in planta development for in-depth analysis. A rare opportunity is given by the developed model system of flax...

The morphogenesis of macromycetes is a complex multilevel process resulting in a set of molecular-genetic, physiologicalbiochemical, and morphological-ultrastructural changes in the cells. When the xylotrophic basidiomycetes Lentinus edodes, Grifola frondosa, and Ganoderma lucidum were grown on wood waste as the substrate, the ultrastructural morph...

The ability to adapt to adverse conditions permits many bacterial species to be virtually ubiquitous and survive in a variety of ecological niches. This ability is of particular importance for many plant pathogenic bacteria that should be able to exist, except for their host plants, in different environments e.g. soil, water, insect-vectors etc. Un...

Modules and pathways of P. atrosepticum genes up-regulated in adapted cells compared to growing ones. (XLS)

Modules and pathways of P. atrosepticum genes down-regulated in adapted cells compared to growing ones. (XLS)

Primers used in this study. (XLS)

Relative expression levels of genes in adapted P. atrosepticum cells vs. growing ones. (XLS)

GO analysis of P. atrosepticum genes up-regulated in adapted cells compared to growing ones (p-value≤0.05). (XLS)

GO analysis of P. atrosepticum genes down-regulated in adapted cells compared to growing ones (p-value≤0.05). (XLS)

Enzymes of CYP74 family play the central role in the biosynthesis of physiologically important oxylipins in land plants. Although a broad diversity of oxylipins is known in the algae, no CYP74s or related enzymes have been detected in brown algae yet. Cloning of the first CYP74-related gene CYP5164B1 of brown alga Ectocarpus siliculosus is reported...

Abscisic acid (ABA) is a well known phytohormone that coordinates abiotic stress responses, water balance and ontogenetic programs in plants. Wherein, ABA was also shown to determine several aspects of plant-microbe interactions. The pathogenesis induced by representatives of Soft-Rot Enterobacteriaceae (SRE), including Pectobacterium atrosepticum...

The representatives of Pectobacterium genus are one of the most harmful phytopathogens in the world. In the present study, we have unraveled novel aspects of plant-Pectobacterium atrosepticum interactions. This bacterium was recently demonstrated to form specific "multicellular" structures - bacterial emboli in the xylem vessels of infected plants....

Bacteria have high adaptive potential that ensures their survival during various environmental challenges. To adapt, bacteria activate a physiological program of stress response that makes them able to persist under adverse conditions. The present study sought to examine the ability of a particular bacterial species to induce a stress response in a...

Activation of expression of the lcc4 and tir genes encoding laccase and tyrosinase was observed during transition of the xylotrophic basidiomycete Lentinus edodes from the vegetative to the generative growth stages. This was especially pronounced in the brown mycelial mat (the stage preceding formation of the fruiting bodies). Development of this s...

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

We report the annotated genome sequence of the enterobacterial plant pathogen Pectobacterium atrosepticum strain 21A, isolated in Belarus from potato stem with blackleg symptoms. FOOTNOTES Address correspondence to Yevgeny Nikolaichik, nikolaichik{at}bio.bsu.by. Citation Nikolaichik Y, Gorshkov V, Gogolev Y, Valentovich L, Evtushenkov A. 2014. Geno...

Enzymes of the CYP74 family, including the divinyl ether synthase (DES), play important roles in plant cell signalling and defence. The potent DES activities have been detected before in the leaves of the meadow buttercup (Ranunculus acris L.) and few other Ranunculaceae species. The nature of these DESs and their genes remained unrevealed. The PCR...

In prokaryotic genomes, the neighboring genes are often located on the complementary DNA strands and adjoin each other by their 5'- or 3'-ends, or even overlap with their open reading frames. It was suggested that this gene topology has a functional purpose of regulating their expression. For the genes that overlap by their coding 3'-end encoding r...

Enzymes of the CYP74 family, including the divinyl ether synthase (DES), play important roles in plant cell signalling and defence. The potent DES activities have been detected before in the leaves of the meadow buttercup (Ranunculus acris L.) and few other Ranunculaceae species. The nature of these DESs and their genes remained unrevealed. The PCR...

The adaptive reactions of plant pathogenic bacterium Pectobacterium atrosepticum SCRI1043 under starvation conditions were studied. The main emphasis was given to the peculiarities of stress responses depending on the bacterial population densities. When bacteria were subjected to starvation at high population densities (10(7)-10(9) CFU ml(-1)), th...

The population dynamics of Pectobacterium atrosepticum SCRI1043 (Pba) within tobacco plants was monitored from the time of inoculation until after long-term preservation of microorganisms in the remnants of dead plants. We found and characterised peculiar structures that totally occlude xylem vessels, which we have named bacterial emboli. Viable bu...