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Varik, Vallo
Publications (6 of 6) Show all publications
Varik, V., Oliveira, S. R., Hauryliuk, V. & Tenson, T. (2017). HPLC-based quantification of bacterial housekeeping nucleotides and alarmone messengers ppGpp and pppGpp. Scientific Reports, 7, Article ID 11022.
Open this publication in new window or tab >>HPLC-based quantification of bacterial housekeeping nucleotides and alarmone messengers ppGpp and pppGpp
2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 11022Article in journal (Refereed) Published
Abstract [en]

Here we describe an HPLC-based method to quantify bacterial housekeeping nucleotides and the signaling messengers ppGpp and pppGpp. We have replicated and tested several previously reported HPLC-based approaches and assembled a method that can process 50 samples in three days, thus making kinetically resolved experiments feasible. The method combines cell harvesting by rapid filtration, followed by acid extraction, freeze-drying with chromatographic separation. We use a combination of C18 IPRP-HPLC (GMP unresolved and co-migrating with IMP; GDP and GTP; AMP, ADP and ATP; CTP; UTP) and SAX-HPLC in isocratic mode (ppGpp and pppGpp) with UV detection. The approach is applicable to bacteria without the requirement of metabolic labelling with 32P-labelled radioactive precursors. We applied our method to quantify nucleotide pools in Escherichia coli BW25113 K12-strain both throughout the growth curve and during acute stringent response induced by mupirocin. While ppGpp and pppGpp levels vary drastically (40-and >= 8-fold, respectively) these changes are decoupled from the quotients of the housekeeping pool and guanosine and adenosine housekeeping nucleotides: NTP/NDP/NMP ratio remains stable at 6/1/0.3 during both normal batch culture growth and upon acute amino acid starvation.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-139786 (URN)10.1038/s41598-017-10988-6 (DOI)000409841100084 ()28887466 (PubMedID)
Available from: 2017-10-03 Created: 2017-10-03 Last updated: 2018-06-09Bibliographically approved
Beljantseva, J., Kudrin, P., Jimmy, S., Ehn, M., Pohl, R., Varik, V., . . . Hauryliuk, V. (2017). Molecular mutagenesis of ppGpp: turning a RelA activator into an inhibitor. Scientific Reports, 7, Article ID 41839.
Open this publication in new window or tab >>Molecular mutagenesis of ppGpp: turning a RelA activator into an inhibitor
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2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 41839Article in journal (Refereed) Published
Abstract [en]

The alarmone nucleotide (p) ppGpp is a key regulator of bacterial metabolism, growth, stress tolerance and virulence, making (p) ppGpp-mediated signaling a promising target for development of antibacterials. Although ppGpp itself is an activator of the ribosome-associated ppGpp synthetase RelA, several ppGpp mimics have been developed as RelA inhibitors. However promising, the currently available ppGpp mimics are relatively inefficient, with IC50 in the sub-mM range. In an attempt to identify a potent and specific inhibitor of RelA capable of abrogating (p) ppGpp production in live bacterial cells, we have tested a targeted nucleotide library using a biochemical test system comprised of purified Escherichia coli components. While none of the compounds fulfilled this aim, the screen has yielded several potentially useful molecular tools for biochemical and structural work.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-132129 (URN)10.1038/srep41839 (DOI)000393552300001 ()28157202 (PubMedID)
Available from: 2017-03-09 Created: 2017-03-09 Last updated: 2018-06-09Bibliographically approved
Kudrin, P., Varik, V., Oliveira, S. R., Beljantseva, J., Santos, T. D., Dzhygyr, I., . . . Hauryliuk, V. (2017). Subinhibitory Concentrations of Bacteriostatic Antibiotics Induce relA-Dependent and relA-Independent Tolerance to beta-Lactams. Antimicrobial Agents and Chemotherapy, 61(4), Article ID e02173-16.
Open this publication in new window or tab >>Subinhibitory Concentrations of Bacteriostatic Antibiotics Induce relA-Dependent and relA-Independent Tolerance to beta-Lactams
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2017 (English)In: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 61, no 4, article id e02173-16Article in journal (Refereed) Published
Abstract [en]

The nucleotide (p) ppGpp is a key regulator of bacterial metabolism, growth, stress tolerance, and virulence. During amino acid starvation, the Escherichia coli (p) ppGpp synthetase RelA is activated by deacylated tRNA in the ribosomal A-site. An increase in (p) ppGpp is believed to drive the formation of antibiotic-tolerant persister cells, prompting the development of strategies to inhibit (p) ppGpp synthesis. We show that in a biochemical system from purified E. coli components, the antibiotic thiostrepton efficiently inhibits RelA activation by the A-site tRNA. In bacterial cultures, the ribosomal inhibitors thiostrepton, chloramphenicol, and tetracycline all efficiently abolish accumulation of (p) ppGpp induced by the Ile-tRNA synthetase inhibitor mupirocin. This abolishment, however, does not reduce the persister level. In contrast, the combination of dihydrofolate reductase inhibitor trimethoprim with mupirocin, tetracycline, or chloramphenicol leads to ampicillin tolerance. The effect is independent of RelA functionality, specific to beta-lactams, and not observed with the fluoroquinolone norfloxacin. These results refine our understanding of (p) ppGpp's role in antibiotic tolerance and persistence and demonstrate unexpected drug interactions that lead to tolerance to bactericidal antibiotics.

Place, publisher, year, edition, pages
AMER SOC MICROBIOLOGY, 2017
Keywords
beta-lactam, RelA, antibiotics, mupirocin, persistence, ppGpp, ribosomes, thiostrepton, tolerance, trimethoprim
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:umu:diva-134211 (URN)10.1128/AAC.02173-16 (DOI)000397598800032 ()28115345 (PubMedID)
Available from: 2017-06-16 Created: 2017-06-16 Last updated: 2018-09-25Bibliographically approved
Andresen, L., Varik, V., Tozawa, Y., Jimmy, S., Lindberg, S., Tenson, T. & Hauryliuk, V. (2016). Auxotrophy-based High Throughput Screening assay for the identification of Bacillus subtilis stringent response inhibitors. Scientific Reports, 6, Article ID 35824.
Open this publication in new window or tab >>Auxotrophy-based High Throughput Screening assay for the identification of Bacillus subtilis stringent response inhibitors
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2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 35824Article in journal (Refereed) Published
Abstract [en]

The stringent response is a central adaptation mechanism that allows bacteria to adjust their growth and metabolism according to environmental conditions. The functionality of the stringent response is crucial for bacterial virulence, survival during host invasion as well as antibiotic resistance and tolerance. Therefore, specific inhibitors of the stringent response hold great promise as molecular tools for disarming and pacifying bacterial pathogens. By taking advantage of the valine amino acid auxotrophy of the Bacillus subtilis stringent response-deficient strain, we have set up a High Throughput Screening assay for the identification of stringent response inhibitors. By screening 17,500 compounds, we have identified a novel class of antibacterials based on the 4-(6-(phenoxy) alkyl)-3,5-dimethyl-1H-pyrazole core. Detailed characterization of the hit compounds as well as two previously identified promising stringent response inhibitors-a ppGpp-mimic nucleotide Relacin and cationic peptide 1018 - showed that neither of the compounds is sufficiently specific, thus motivating future application of our screening assay to larger and more diverse molecular libraries.

National Category
Microbiology Infectious Medicine
Identifiers
urn:nbn:se:umu:diva-127600 (URN)10.1038/srep35824 (DOI)000385923600001 ()27775002 (PubMedID)
Available from: 2016-12-07 Created: 2016-11-16 Last updated: 2018-06-09Bibliographically approved
Varik, V., Oliveira, S. R., Hauryliuk, V. & Tenson, T. (2016). Composition of the outgrowth medium modulates wake-up kinetics and ampicillin sensitivity of stringent and relaxed Escherichia coli. Scientific Reports, 6, Article ID 22308.
Open this publication in new window or tab >>Composition of the outgrowth medium modulates wake-up kinetics and ampicillin sensitivity of stringent and relaxed Escherichia coli
2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 22308Article in journal (Refereed) Published
Abstract [en]

The transition of Escherichia coli from the exponential into the stationary phase of growth induces the stringent response, which is mediated by the rapid accumulation of the alarmone nucleotide (p)ppGpp produced by the enzyme RelA. The significance of RelA's functionality during the transition in the opposite direction, i.e. from the stationary phase into new exponential growth, is less well understood. Here we show that the relaxed strain, i.e. lacking the relA gene, displays a relative delay in regrowth during the new exponential growth phase in comparison with the isogenic wild type strain. The severity of the effect is a function of both the carbon source and amino acid composition of the outgrowth media. As a result, the loss of RelA functionality increases E. coli tolerance to the bactericidal antibiotic ampicillin during growth resumption in fresh media in a medium-specific way. Taken together, our data underscore the crucial role of medium composition and growth conditions for studies of the role of individual genes and regulatory networks in bacterial phenotypic tolerance to antibiotics.

National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-118391 (URN)10.1038/srep22308 (DOI)000371023500004 ()
Available from: 2016-04-18 Created: 2016-03-18 Last updated: 2018-06-07Bibliographically approved
Monteferrante, C. G., Jirgensons, A., Varik, V., Hauryliuk, V., Goessens, W. H. & Hays, J. P. (2016). Evaluation of the characteristics of leucyl-tRNA synthetase (LeuRS) inhibitor AN3365 in combination with different antibiotic classes. European Journal of Clinical Microbiology and Infectious Diseases, 35(11), 1857-1864
Open this publication in new window or tab >>Evaluation of the characteristics of leucyl-tRNA synthetase (LeuRS) inhibitor AN3365 in combination with different antibiotic classes
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2016 (English)In: European Journal of Clinical Microbiology and Infectious Diseases, ISSN 0934-9723, E-ISSN 1435-4373, Vol. 35, no 11, p. 1857-1864Article in journal (Refereed) Published
Abstract [en]

Aminoacyl tRNA synthetases are enzymes involved in the key process of coupling an amino acid to its cognate tRNA. AN3365 is a novel antibiotic that specifically targets leucyl-tRNA synthetase, whose development was halted after evaluation in phase II clinical trials owing to the rapid selection of resistance. In an attempt to bring AN3365 back into the developmental pipeline we have evaluated the efficacy of AN3365 in combination with different classes of antibiotic and characterized its mechanism of action. Although we detect no synergy or antagonism in combination with a range of antibiotic classes, a combination of AN3365 with colistin reduces the accumulation of AN3365-resistant and colistin resistance mutations. We also demonstrate that treatment with AN3365 results in the dramatic accumulation of the alarmone (p)ppGpp, the effector of the stringent response-a key player in antibiotic tolerance.

National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-129885 (URN)10.1007/s10096-016-2738-1 (DOI)000386157300018 ()27506217 (PubMedID)
Available from: 2017-01-16 Created: 2017-01-10 Last updated: 2018-06-09Bibliographically approved
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