A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding

Terekhov, Stanislav S.; Mokrushina, Yuliana A.; Nazarov, Anton; Zlobin, Alexander; Zalevsky, Arthur O.; Bourenkov, Gleb; Golovin, Andrey V.; Belogurov, Alexey A.; Osterman, Ilya А.; Kulikova, Alexandra A.; Mitkevich, Vladimir A.; Lou, Hua; Turk, Benjamin E.; Wilmanns, Matthias; Смирнов, Иван; Altman, Sidney; Gabibov, Alexander

doi:10.1126/sciadv.aaz9861

Cited by 18 publications

(16 citation statements)

References 71 publications

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“…The human oral cavity is one of the most exciting microbial habitats. Over 700 microbial species inhabiting the oral cavity and forming unique communities have been found [ 5 , 6 , 7 ]. The composition of such communities is relatively stable for the healthy oral cavity [ 8 ] and plays an important role in maintaining a dynamic ecological balance with the host [ 9 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

Drift of the Subgingival Periodontal Microbiome during Chronic Periodontitis in Type 2 Diabetes Mellitus Patients

et al. 2021

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Since periodontitis and type 2 diabetes mellitus are complex diseases, a thorough understanding of their pathogenesis requires knowing the relationship of these pathologies with other disorders and environmental factors. In this study, the representability of the subgingival periodontal microbiome of 46 subjects was studied by 16S rRNA gene sequencing and shotgun sequencing of pooled samples. We examined 15 patients with chronic periodontitis (CP), 15 patients with chronic periodontitis associated with type 2 diabetes mellitus (CPT2DM), and 16 healthy subjects (Control). The severity of generalized chronic periodontitis in both periodontitis groups of patients (CP and CPT2DM) was moderate (stage II). The male to female ratios were approximately equal in each group (22 males and 24 females); the average age of the subjects was 53.9 ± 7.3 and 54.3 ± 7.2 years, respectively. The presence of overweight patients (Body Mass Index (BMI) 30–34.9 kg/m2) and patients with class 1–2 obesity (BMI 35–45.9 kg/m2) was significantly higher in the CPT2DM group than in patients having only chronic periodontitis or in the Control group. However, there was no statistically significant difference in all clinical indices between the CP and CPT2DM groups. An analysis of the metagenomic data revealed that the alpha diversity in the CPT2DM group was increased compared to that in the CP and Control groups. The microbiome biomarkers associated with experimental groups were evaluated. In both groups of patients with periodontitis, the relative abundance of Porphyromonadaceae was increased compared to that in the Control group. The CPT2DM group was characterized by a lower relative abundance of Streptococcaceae/Pasteurellaceae and a higher abundance of Leptotrichiaceae compared to those in the CP and Control groups. Furthermore, the CP and CPT2DM groups differed in terms of the relative abundance of Veillonellaceae (which was decreased in the CPT2DM group compared to CP) and Neisseriaceae (which was increased in the CPT2DM group compared to CP). In addition, differences in bacterial content were identified by a combination of shotgun sequencing of pooled samples and genome-resolved metagenomics. The results indicate that there are subgingival microbiome-specific features in patients with chronic periodontitis associated with type 2 diabetes mellitus.

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Section: Introductionmentioning

confidence: 99%

Drift of the Subgingival Periodontal Microbiome during Chronic Periodontitis in Type 2 Diabetes Mellitus Patients

et al. 2021

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“…The most refined method to avoid mispairing is based on amplification of single DNA molecules encapsulated inside isolated microcompartments of water-in-oil emulsions. Compartmentalization provides critical advantages to droplet-based single-cell technologies, namely the ability to distinguish and select rare individual clones from the enormous biodiversity ( 7 – 10 ). Similarly, pioneering work on single-molecule PCR amplification opened the era of emulsion PCR (ePCR) ( 11 ), which was successfully applied to amplifying complex gene libraries ( 12 ), PCR on microparticles in water-in-oil emulsions ( 13 ), and directed evolution driven by in vitro compartmentalization ( 14 ).…”

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confidence: 99%

Liquid drop of DNA libraries reveals total genome information

Terekhov

Eliseev

Ovchinnikova

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Conventional “bulk” PCR often yields inefficient and nonuniform amplification of complex templates in DNA libraries, introducing unwanted biases. Amplification of single DNA molecules encapsulated in a myriad of emulsion droplets (emulsion PCR, ePCR) allows the mitigation of this problem. Different ePCR regimes were experimentally analyzed to identify the most robust techniques for enhanced amplification of DNA libraries. A phenomenological mathematical model that forms an essential basis for optimal use of ePCR for library amplification was developed. A detailed description by high-throughput sequencing of amplified DNA-encoded libraries highlights the principal advantages of ePCR over bulk PCR. ePCR outperforms PCR, reduces gross DNA errors, and provides a more uniform distribution of the amplified sequences. The quasi single-molecule amplification achieved via ePCR represents the fundamental requirement in case of complex DNA templates being prone to diversity degeneration and provides a way to preserve the quality of DNA libraries.

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“…An extensive number of cryptic AR enzymes yet to be discovered [ 38 ] and resistance toward lysostaphin was documented for laboratory strains [ 19 , 39 ]. The major mechanism of acquired lysostaphin resistance relates to mutations in the femA gene, which encodes the factor responsible for the addition of the second and third glycines to the pentaglycine bridge of the cell wall [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

Selective Eradication of Staphylococcus aureus by the Designer Genetically Programmed Yeast Biocontrol Agent

et al. 2020

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Staphylococcus aureus is a common human pathogen that is particularly often associated with antibiotic resistance. The eradication of this ubiquitous infectious agent from its ecological niches and contaminated surfaces is especially complicated by excessive biofilm formation and persisting cells, which evade the antibacterial activity of conventional antibiotics. Here, we present an alternative view of the problem of specific S. aureus eradication. The constitutive heterologous production of highly specific bacteriolytic protease lysostaphin in yeast Pichia pastoris provides an efficient biocontrol agent, specifically killing S. aureus in coculture. A yeast-based anti-S. aureus probiotic was efficient in a high range of temperatures and target-to-effector ratios, indicating its robustness and versatility in eliminating S. aureus cells. The efficient eradication of S. aureus by live lysostaphin-producing P. pastoris was achieved at high scales, providing a simple, biocompatible and cost-effective strategy for S. aureus lysis in bioproduction and surface decontamination. Future biomedical applications based on designer yeast biocontrol agents require evaluation in in vivo models. However, we believe that this strategy is very promising since it provides highly safe, efficient and selective genetically programmed probiotics and targeted biocontrol agents.

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A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding

Cited by 18 publications

References 71 publications

Drift of the Subgingival Periodontal Microbiome during Chronic Periodontitis in Type 2 Diabetes Mellitus Patients

Drift of the Subgingival Periodontal Microbiome during Chronic Periodontitis in Type 2 Diabetes Mellitus Patients

Liquid drop of DNA libraries reveals total genome information

Selective Eradication of Staphylococcus aureus by the Designer Genetically Programmed Yeast Biocontrol Agent

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