Abstract Numerous studies are devoted to the intestinal microbiota and intercellular communication maintaining homeostasis. In this regard, vesicles secreted by bacteria represent one of most popular topics for research. For example, outer membrane (OMVs) Bacteroides fragilis play an important nutritional role with respect other microorganisms promote anti-inflammatory effects on immune cells. However, toxigenic B. (ETBF) contributes bowel disease, even causing colon cancer. If nontoxigenic...

Currently, synthetic genomics is a rapidly developing field. Its main tasks, such as the design of sequences and assembly DNA from oligonucleotides, require specialized software. In this article, we present program with graphical interface that allows non-bioinformatics to perform tasks needed in genomics. We developed BAC-browser v.2.1. It helps nucleotide features following tools: generate sequence amino acid using codon frequency table for specific organism, well visualization restriction...

The avian bacterial pathogen Mycoplasma gallisepticum is a good model for systems studies due to small genome and simplicity of regulatory pathways. In this study, we used RNA-Seq MS-based proteomics accurately map coding sequences, transcription start sites (TSSs) transcript 3′-ends (T3Es). We obtained data investigate roles TSSs T3Es in stress-induced transcriptional responses. identified 1061 at false discovery rate 10% showed that almost all M. initiated from classic TATAAT promoters...

New oligonucleotide analogues with triazole internucleotide linkages were synthesized, and their hybridization properties studied. The demonstrated DNA binding affinities similar to those of unmodified oligonucleotides. modification was shown protect the oligonucleotides from nuclease hydrolysis. modified tested as PCR primers. Modifications remote 3′-terminus tolerated by polymerases. Our results suggest that these new are among most promising mimics characterized date.

DNA repair is essential for the maintenance of genome stability in all living beings. Genome size as well repertoire and abundance components may vary among prokaryotic species. The bacteria Mollicutes class feature a small size, absence cell wall, parasitic lifestyle. A number genes make good model "minimal cell" concept.In this work we studied system Mycoplasma gallisepticum on genomic, transcriptional, proteomic levels. We detected 18 out 22 members protein level. found that respective...

Abstract What strategies do bacteria employ for adaptation to their hosts and are these different varied hosts? To date, many studies on the interaction of bacterium its host have been published. However, global changes in bacterial cell process invasion persistence, remain poorly understood. In this study, we demonstrated phase transition avian pathogen Mycoplasma gallisepticum upon various types eukaryotic cells (human, chicken, mouse) which was stable during several passages after...

Mollicutes (mycoplasmas) have been recognized as highly evolved prokaryotes with an extremely small genome size and very limited coding capacity. Thus, they may serve a model of 'minimal cell': cell the lowest possible number genes yet capable autonomous self-replication. We present results comparative analysis proteomes three mycoplasma species: A. laidlawii, M. gallisepticum, mobile. The core proteome components found in species are involved fundamental cellular processes which necessary...

Mollicutes (mycoplasmas) feature a significant loss of known regulators gene expression. Here, we identified the recognition site MraZ-family regulator Mycoplasma gallisepticum, which is conserved in many species different clades within class Mollicutes. The MraZ binding AAAGTG[T/G], promoter mraZ it forms series direct repeats with structure (AAAGTG[T/G]N3)k, where k = 3 most frequently. binds to single repeat as an octamer complex. can also bind or spacer lengths (2-4 nt); thus, may play...

We present a systematic study of three bacterial species that belong to the class Mollicutes, smallest and simplest bacteria, Spiroplasma melliferum, Mycoplasma gallisepticum, Acholeplasma laidlawii. To understand difference in basic principles metabolism regulation adaptation environmental conditions species, we analyzed metabolome these bacteria. Metabolic pathways were reconstructed using proteogenomic annotation data provided by our lab. The results metabolome, proteome genome profiling...

Crohn's disease (CD) is a severe chronic immune-mediated granulomatous inflammatory of the gastrointestinal tract. The mechanisms CD pathogenesis remain obscure. Metagenomic analysis samples from patients revealed that several them have elevated level

The Twort-like myoviruses (

Prokaryotes are actively studied objects in the scope of genomic regulation. Microbiologists need special tools for complex analysis data to study and identification regulatory mechanism bacteria archaea. We developed a tool BAC-BROWSER, specifically visualization small prokaryotic genomes. BAC-BROWSER provides different types wide set mechanisms prokaryotes: -transcriptional regulation by transcription factors (TFs), TFs, their targets, binding sites.-other motifs, promoters, terminators...

Bacteria of the class Mollicutes have significantly reduced genomes and gene expression control systems. They are also efficient pathogens that can colonize a broad range hosts including plants animals. Despite their simplicity, demonstrate complex transcriptional responses to various conditions, which contradicts reduction in regulation mechanisms. We analyzed conservation distribution transcription regulators across 50 species. The majority factors regulate transport metabolism, there four...

Introduction.Mycoplasma hominis is a bacterium belonging to the class Mollicutes. It causes acute and chronic infections of urogenital tract. The main features this are an absence cell wall reduced genome size (517-622 protein-encoding genes). Previously, we have isolated morphologically unknown M. colonies called micro-colonies (MCs) from serum patients with inflammatory tract infection.Hypothesis. MCs functionally different typical (TCs) in terms metabolism division.Aim. To determine...

At present, bacteriophages are considered as an alternative to antibiotics in prevention and treatment of bacterial infections, particular cholera. The aim the work was demonstrate a method obtain synthetic bacteriophage against Vibrio cholerae . Vibriophage N4 selected subject for study. Materials methods genome sequence vibriophage (38.5 kb) taken from NCBI GenBank database. divided into gene blocks 1500–2000 bp. blocks, turn, were split oligonucleotides. Sequence partitioning carried out...

The standardization of DNA fragment assembly methods for many tasks synthetic biology is crucial. This necessary synthesizing a wider repertoire sequences, as well further automation and miniaturization such reactions. In this work, we proposed conditions the fragments from chemically synthesized oligonucleotides identified errors occurring in sequence under these conditions. Additionally, combining into larger fragments. We showed that optimized are suitable wide range sequences.

BACKGROUND: Mammalian cell cultures play a key role in the pharmaceutical industry, requiring constant monitoring of conditions during fermentation. In addition to physical-chemical parameters, it is important evaluate internal state cells, for which gene expression analysis used. Currently, quantitative reverse transcription polymerase chain reaction (qPCR) dominant method. However, loop-mediated isothermal amplification (LAMP) technique also attracts attention due its high specificity,...

Introduction WhiA is a conserved protein found in numerous bacteria. It consists of an HTH DNA-binding domain linked with homing endonuclease (HEN) domain. one the most transcription factors reduced bacteria class Mollicutes. Its function Mollicutes unknown, while it well-characterized Streptomyces . Here, we focused on from Mycoplasma gallisepticum Methods We used combination molecular dynamics, EMSA, MST and AFM to study ATP-binding properties M. The transcriptional repressor was...

Mycoplasma hominis is an opportunistic urogenital pathogen in vertebrates. It a non-glycolytic species that produces energy via arginine degradation. Among genital mycoplasmas, M. the most commonly reported to play role systemic infections and can persist host for long time. However, it unclear how proceeds under limitation. The recent metabolic reconstruction of has demonstrated its ability catabolize deoxyribose phosphate produce ATP. In this study, we cultivated on two different sources...

The epigenetics of bacteria, and bacteria with a reduced genome in particular, is great interest, but still poorly understood. Mycoplasma gallisepticum, representative the class Mollicutes, an excellent model minimal cell because its size, lack wall, primitive organization. In this study we investigated DNA modifications object gallisepticum their roles. We identified methylation motifs M. S6 at level using single molecule real time (SMRT) sequencing. Only ANCNNNNCCT motif was found genome....

Bacteria of class Mollicutes (mycoplasmas) feature significant genome reduction which makes them good model organisms for systems biology studies. Previously we demonstrated, that drastic transcriptional response mycoplasmas to stress results in a very limited on the level protein. In this study used heat M. gallisepticum and ribosome profiling elucidate process genetic information transfer under stress. We found ribosomes demonstrate selectivity towards mRNA binding. identified may be...

Mycoplasmas are pathogenic, genome-reduced bacteria. The development of such fields science as system and synthetic biology is closely associated with them. Despite intensive research different representatives this genus, genetic manipulations remain challenging in mycoplasmas. Here we demonstrate a single-plasmid transposon-based CRISPRi for the repression gene expression We show that selected determinants provide level dCas9 does not lead to significant slow-down mycoplasma growth. For...

Abstract Despite the fact term “proteome” was proposed to characterize a set of proteins in one mycoplasma species, proteome response various exposures this bacteria are still obscure. Commonly, authors studying proteomic on perturbation models mycoplasmas use single approach and do not confirm their findings by alternative methods. Consequently, results analysis should be validated complementary techniques. In study we utilized three approaches (SWATH, MRM, 2D-DIGE) assess Mycoplasma...

Mycoplasma gallisepticum is an intracellular parasite affecting respiratory tract of poultry that belongs to class Mollicutes. M. features numerous variable lipoprotein hemagglutinin genes (vlhA) play a role in immune escape. The vlhA promoters have set distinct properties comparison the other genes. carry GAA repeats region at approximately 40 nts upstream transcription start site. been considered active only presence exactly 12 repeats. mechanisms expression regulation and number variation...