Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy

Bespyatykh, Julia; Shitikov, Egor; Bespiatykh, Dmitry; Guliaev, Andrei; Klimina, Ksenia M.; Veselovsky, Vladimir A.; Arapidi, Georgij; Dogonadze, Marine; Zhuravlev, Viacheslav; Ilina, Elena; Govorun, Vadim M.

doi:10.3390/pathogens9020131

Cited by 13 publications

(8 citation statements)

References 47 publications

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“…RNA sequencing and analysis were performed as previously described [ 27 ] with some modification. Total RNA (1 μg) was used for library preparation.…”

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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“…RNA sequencing and analysis were performed as previously described [ 27 ] with some modification. Total RNA (1 μg) was used for library preparation.…”

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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“…Total RNA (1 μg) was used for library preparation as previously described ( Bespyatykh et al, 2020 ) with some modifications. Ribosomal RNA was removed from the total RNA using the Ribo-Zero Plus rRNA Depletion Kit (Illumina, United States) and libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB), according to the manufacturer’s protocol.…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic Profile of Mycobacterium smegmatis in Response to an Imidazo[1,2-b][1,2,4,5]tetrazine Reveals Its Possible Impact on Iron Metabolism

et al. 2021

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Tuberculosis (TB), caused by the Mycobacterium tuberculosis complex bacteria, is one of the most pressing health problems. The development of new drugs and new therapeutic regimens effective against the pathogen is one of the greatest challenges in the way of tuberculosis control. Imidazo[1,2-b][1,2,4,5]tetrazines have shown promising activity against M. tuberculosis and M. smegmatis strains. Mutations in MSMEG_1380 lead to mmpS5–mmpL5 operon overexpression, which provides M. smegmatis with efflux-mediated resistance to imidazo[1,2-b][1,2,4,5]tetrazines, but the exact mechanism of action of these compounds remains unknown. To assess the mode of action of imidazo[1,2-b][1,2,4,5]tetrazines, we analyzed the transcriptomic response of M. smegmatis to three different concentrations of 3a compound: 1/8×, 1/4×, and 1/2× MIC. Six groups of genes responsible for siderophore synthesis and transport were upregulated in a dose-dependent manner, while virtual docking revealed proteins involved in siderophore synthesis as possible targets for 3a. Thus, we suggest that imidazo[1,2-b][1,2,4,5]tetrazines may affect mycobacterial iron metabolism.

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“…Data processing and analysis were performed as previously described ( 29 ). Quality control of raw reads was carried out with FASTQC v0.11.5.…”

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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Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy

Cited by 13 publications

References 47 publications

Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1

Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1

Transcriptomic Profile of Mycobacterium smegmatis in Response to an Imidazo[1,2-b][1,2,4,5]tetrazine Reveals Its Possible Impact on Iron Metabolism

Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors

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