BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes

Garanina, Irina; Fisunov, Gleb Y.; Govorun, Vadim M.

doi:10.3389/fmicb.2018.02827

Cited by 17 publications

(10 citation statements)

References 44 publications

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“…For the identification of promoters and terminators, the coverage was visualized and analyzed using the BAC-BROWSER tool [ 37 ]. The reads, oriented against the transcription direction (R2 reads), were used to search for the putative transcription start sites (TSSs) prediction, and the transcription-wise R1 reads were used for the transcriptional termination sites (TTSs) prediction.…”

Section: Methodsmentioning

confidence: 99%

Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1

Kornienko

Fisunov

Bespiatykh

et al. 2020

Viruses

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The Twort-like myoviruses (Kayvirus genus) of S. aureus are promising agents for bacteriophage therapy due to a broad host range and high killing activity against clinical isolates. This work improves the current understanding of the phage infection physiology by transcriptome analysis. The expression profiles of a typical member of the Kayvirus genus (vB_SauM-515A1) were obtained at three time-points post-infection using RNA sequencing. A total of 35 transcription units comprising 238 ORFs were established. The sequences for 58 early and 12 late promoters were identified in the phage genome. The early promoters represent the strong sigma-70 promoters consensus sequence and control the host-dependent expression of 26 transcription units (81% of genes). The late promoters exclusively controlled the expression of four transcription units, while the transcription of the other five units was directed by both types of promoters. The characteristic features of late promoters were long -10 box of TGTTATATTA consensus sequence and the absence of -35 boxes. The data obtained are also of general interest, demonstrating a strategy of the phage genome expression with a broad overlap of the early and late transcription phases without any middle transcription, which is unusual for the large phage genomes (>100 kbp).

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Section: Methodsmentioning

confidence: 99%

Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1

Kornienko

Fisunov

Bespiatykh

et al. 2020

Viruses

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“…Primers used are listed in Supplementary Table S1 . All primers were designed using BAC-Browser ( Garanina et al, 2018 ). Each 20-μl reaction contained 0.2 μl of template cDNA.…”

Section: Methodsmentioning

confidence: 99%

Propionate Induces Virulent Properties of Crohn’s Disease-Associated Escherichia coli

et al. 2020

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Crohn’s disease (CD) is a severe chronic immune-mediated granulomatous inflammatory disease of the gastrointestinal tract. The mechanisms of CD pathogenesis remain obscure. Metagenomic analysis of samples from CD patients revealed that several of them have the elevated level of Escherichia coli with adhesive–invasive phenotype (AIEC). Previously, we isolated an E. coli strain CD isolate ZvL2 from a patient with CD, which features AIEC phenotype. Here, we demonstrate that prolonged growth on propionate containing medium stimulates virulent properties of CD isolate ZvL2, while prolonged growth on glucose reduces these properties to levels indistinguishable from laboratory strain K-12 MG1655. Propionate presence also boosts the ability of CD isolate ZvL2 to penetrate and colonize macrophages. The effect of propionate is reversible, re-passaging of CD isolate on M9 medium supplemented with glucose leads to the loss of its virulent properties. Proteome analysis of CD isolate ZvL2 growth in medium supplemented with propionate or glucose revealed that propionate induces expression porins OmpA and OmpW, transcription factors PhoP and OmpR , and universal stress protein UspE , which were previously found to be important for macrophage colonization by enteropathogenic bacteria.

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“…SAM files processing was performed by samtools ( 35 ). Identification of TSS and subsequent analysis were performed from sam files with BAC-Browser ( 36 ) with standard parameters.…”

Section: Methodsmentioning

confidence: 99%

Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors

et al. 2020

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As permanent residents of the normal gut microbiota, bifidobacteria have evolved to adapt to the host’s immune response whose priority is to eliminate pathogenic agents. The mechanisms that ensure the survival of commensals during inflammation and maintain the stability of the core component of the normal gut microbiota in such conditions remain poorly understood. We propose a new in vitro approach to study the mechanisms of resistance to immune response factors based on high-throughput sequencing followed by transcriptome analysis. This approach allowed us to detect differentially expressed genes associated with inflammation. In this study, we demonstrated that the presence of the pro-inflammatory cytokines IL-6 and TNFα to the growth medium of the B. longum subsp. longum GT15 strain changes the latter’s growth rate insignificantly while affecting the expression of certain genes. We identified these genes and performed a COG and a KEGG pathway enrichment analysis. Using phylogenetic profiling we predicted the operons of genes whose expression was triggered by the cytokines TNFα and IL-6 in vitro . By mapping the transcription start points, we experimentally validated the predicted operons. Thus, in this study, we predicted the genes involved in a putative signaling pathway underlying the mechanisms of resistance to inflammatory factors in bifidobacteria. Since bifidobacteria are a major component of the human intestinal microbiota exhibiting pronounced anti-inflammatory properties, this study is of great practical and scientific relevance.

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BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes

Cited by 17 publications

References 44 publications

Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1

Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1

Propionate Induces Virulent Properties of Crohn’s Disease-Associated Escherichia coli

Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors

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