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Daptomycin tolerance in the Staphylococcus aureus pitA6 mutant is due to upregulation of the dlt-operon

ABSTRACT: It is very important to understand the mechanisms how bacteria become tolerant towards antibiotics during clinical therapy. In a previous study we showed that increased daptomycin (DAP) tolerance of Staphylococcus aureus was due to a point mutation in pitA (inorganic phosphate transporter) that led to intracellular accumulation of both inorganic phosphate (Pi) and polyphosphate (polyP). DAP tolerance in that pitA6 mutant differs from classical resistance mechanisms as there was no increase in minimal inhibitory concentration (MIC). In this study we demonstrate that DAP tolerance in the pitA6 mutant is not triggered by the accumulation of polyP. Transcriptome analysis revealed that about 234 genes were at least 2.0-fold differently expressed in the mutant. Particularly, genes involved in protein biosynthesis, carbohydrate and lipid metabolism as well as in replication and maintenance of DNA were downregulated. However, the most important change was the upregulation of the dlt-operon, which is induced by the accumulation of intracellular Pi. The GraXRS system, known as activator of both dlt and mprF, as well as surface charge, cell wall thickness or the content of wall teichoic acids (WTA) are not involved in DAP tolerance in the pitA6 mutant. In conclusion the DAP tolerance in the pitA6 mutant is due to an upregulation of the dlt-operon triggered directly or indirectly by the accumulation of Pi.

ORGANISM(S): Staphylococcus aureus

PROVIDER: GSE77069 | GEO | 2016/02/10

SECONDARY ACCESSION(S): PRJNA309388

REPOSITORIES: GEO

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Daptomycin tolerance in the Staphylococcus aureus pitA6 mutant is due to upregulation of the dlt-operon

Project description:It is very important to understand the mechanisms how bacteria become tolerant towards antibiotics during clinical therapy. In a previous study we showed that increased daptomycin (DAP) tolerance of Staphylococcus aureus was due to a point mutation in pitA (inorganic phosphate transporter) that led to intracellular accumulation of both inorganic phosphate (Pi) and polyphosphate (polyP). DAP tolerance in that pitA6 mutant differs from classical resistance mechanisms as there was no increase in minimal inhibitory concentration (MIC). In this study we demonstrate that DAP tolerance in the pitA6 mutant is not triggered by the accumulation of polyP. Transcriptome analysis revealed that about 234 genes were at least 2.0-fold differently expressed in the mutant. Particularly, genes involved in protein biosynthesis, carbohydrate and lipid metabolism as well as in replication and maintenance of DNA were downregulated. However, the most important change was the upregulation of the dlt-operon, which is induced by the accumulation of intracellular Pi. The GraXRS system, known as activator of both dlt and mprF, as well as surface charge, cell wall thickness or the content of wall teichoic acids (WTA) are not involved in DAP tolerance in the pitA6 mutant. In conclusion the DAP tolerance in the pitA6 mutant is due to an upregulation of the dlt-operon triggered directly or indirectly by the accumulation of Pi. WT strain HG003 and its pitA mutant were used to compare transcriptomic changes after 6 or 8 hours of growth in suspension in TSB medium

2016-02-10 | E-GEOD-77069 | biostudies-arrayexpress

Changes in relative transcript amounts caused by ∆phoU2::kanrpsL+ and double ∆phoU2::kanrpsL+ ∆phoU1::Pcerm mutations in Streptococcus pneumoniae

Project description:Unlike most bacteria, Streptococcus pneumoniae (pneumococcus) has two evolutionarily distinct ABC transporters (Pst1 and Pst2) for inorganic phosphate (Pi) uptake. The genes encoding a two-component regulator (PnpRS) are located immediately upstream of the pst1 operon. Both the pst1 and pst2 operons encode putative PhoU regulators (PhoU1 and PhoU2) at their ends.his study addresses why S. pneumoniae contains dual Pi uptake systems and the regulation and contribution of the Pst1 and Pst2 systems in conditions of high (mM) Pi amount and low (μM) Pi amount. To determine whether PhoU1 or PhoU2 regulates pnpRS, pst1, or pst2 operons. we performed RNA-Seq analyses of ΔphoU2::kanrpsL+ sinlge mutant and ΔphoU2::kanrpsL+ ΔphoU1::Pcerm double mutant compared to the isogenic encapsulated strain cep::kanrpsL+. Unexpectedly, only ΔphoU2::kanrpsL+ indulces the pst1 operon, but not pst2 or pnpRS operon. Addtional PhoU1 deletion has no effect on pst1, pst2, or pnpRS operons.

2017-02-14 | GSE80637 | GEO

Escherichia coli O157:H7 responds to phosphate starvation by modifying LPS involved in biofilm formation

Project description:Pathogens like E. coli O157:H7 are responsible for many outbreaks and can be found and survive in poor inorganic phosphate (Pi) environments. In E. coli the phosphate homeostasis is regulated by the Pst system and the two-component system PhoB/R. In a Δpst mutant, PhoB is constitutively activated and biofilm formation is increased. To understand how PhoB activation lead to biofilm increase, we compared the transcriptomes of EDL933 the WT strain and Δpst mutant both grown in MOPS Pi rich medium, using the Affymetrix GeneChip® E. coli Genome 2.0 Array.

2019-01-23 | GSE125488 | GEO

Blue light regulates phosphate deficiency-dependent primary root growth inhibition in Arabidopsis

Project description:Plants have evolved mechanisms to improve utilization efficiency or acquisition of inorganic phosphate (Pi) in response to Pi deficiency, such as altering root architecture, secreting acid phosphatases, and activating the expression of genes related to Pi uptake and recycling. Although many genes responsive to Pi starvation have been identified, transcription factors that affect tolerance to Pi deficiency have not been well characterized. We show here that the ectopic expression of B-BOX32 (BBX32) and the mutation of ELONGATED HYPOCOTYL 5 (HY5), whose transcriptional activity is negatively regulated by BBX32, resulted in the tolerance to Pi deficiency in Arabidopsis. The primary root lengths of 35S:BBX32 and hy5 plants were only slightly inhibited under Pi deficient condition and the fresh weights were significantly higher than those of wild type. The Pi deficiency-tolerant root phenotype of hy5 was similarly observed when grown on the medium without Pi. In addition, a double mutant, hy5 slr1, without lateral roots also showed a long primary root phenotype under phosphate deficiency, indicating that the root phenotype of hy5 does not result from increase of external Pi uptake. Moreover, we found that blue light may regulate Pi deficiency-dependent primary root growth inhibition through activating peroxidase gene expression, suggesting the Pi-deficiency tolerant root phenotype of hy5 may be due to blockage of blue-light responses. Altogether, this study points out light quality may play an important role in the regulation of Pi deficiency responses. It may contribute to regulate plant growth under Pi deficiency through a proper illumination.

2019-11-27 | GSE139100 | GEO

PhoB Activates Escherichia coli O157:H7 Virulence Factors in Response to Inorganic Phosphate Limitation

Project description:In E. coli the phosphate homeostasis is regulated by the Pst system and the two-component system PhoB/R. Pathogens like E. coli O157:H7 are responsible for many outbreaks and can be found and survive in poor inorganic phosphate (Pi) environments. To understand global EHEC O157:H7 EDL933 strain responses to Pi-starvation, we compared the transcriptomes of EDL933 the WT strain grown in MOPS Pi rich medium and that grown in MOPS Pi poor medium, using the Affymetrix GeneChip® E. coli Genome 2.0 Array. Also we investigated the EDL933 global response to the absence of PhoB by comparing the transcriptomes of the WT strain the ΔphoB mutant both grown in Low Pi

2014-03-15 | GSE50529 | GEO

A broad response to intracellular long-chain polyphosphate in human cells

Project description:Polyphosphates (PolyP) are highly anionic, linear polymers composed of long chains of inorganic phosphates linked together by phosphoanhydride bonds. PolyP chains are found in all kingdoms of life, and play roles in phosphate homeostasis, cell growth, infection, and blood coagulation. Unlike in bacteria and yeast, the mammalian enzymes responsible for the synthesis and degradation of polyP are unknown, which presents a challenge for the study of polyP in higher eukaryotes. To overcome this, we use a system to produce polyP inside of human cells through the ectopic expression of the E. coli Ppk1 synthetic enzyme. Here, we present the results from large-scale transcriptomic and proteomic analyses of polyP producing HEK293T cells. We uncovered >350 RNAs and 14 proteins that show changes following in vivo polyP accumulation. Follow up on specific hits revealed that the internal accumulation of polyP resulted in a significant decrease in the dehydrogenase/reductase DHRS2 without a corresponding increase in p53 phosphorylation, and activation of the ERK1/2-ERG1 signaling axis. Finally, following upregulation of internal polyP we observed the relocalization and redistribution of several nuclear proteins, including chromatin bound proteins DEK, TAF10, GTF2I and the translation initiation factor eIF5b. Altogether, our work serves as a novel resource to understand the impact of increased intracellular polyP in mammalian cells.

2020-09-24 | PXD018896 | Pride

A. fumigatus wild type and delta phoB(PHO80) strains transcriptome analysis for growth upon minimal medium 0.1 mM Pi

Project description:Phosphate is an essential ion for fungal growth, required for proper DNA and phospholipids biosyntesis, energetic metabolism and signal transduction. The systems for inorganic phosphate (Pi) acquisition in eukaryotic cells (PHO) have been characterized as a low-affinity (that assures a supply of Pi at normal or high external Pi concentrations) and a high-affinity (activated in response to Pi starvation). Here, as an initial step to understand the PHO pathway in A. fumigatus, we characterized the PHO80 homologue, phoB(PHO80). We showed that the delta phoB(PHO80) mutant has a severe polar growth defect and there is an interaction between PhoB(PHO80), calcineurin and calcium metabolism. Microarray hybridizations carried out with RNA obtained from wild type and delta phoB(PHO80) mutant cells showed that Afu4g03610 [phoD(PHO84)], Afu7g06350 [phoE9(PHO89)], Afu4g06020 [phoCPHO81)], and Afu2g09040 (vacuolar transporter Vtc4) were more expressed either in the delta phoB(PHO80) mutant background or in 0.1 mM Pi. Keywords: gene expression array-based (log2 ratio)

2007-11-09 | GSE9548 | GEO

A. fumigatus wild type and delta phoB(PHO80) strains transcriptome analysis for growth upon minimal medium 11 mM Pi

Project description:Phosphate is an essential ion for fungal growth, required for proper DNA and phospholipids biosyntesis, energetic metabolism and signal transduction. The systems for inorganic phosphate (Pi) acquisition in eukaryotic cells (PHO) have been characterized as a low-affinity (that assures a supply of Pi at normal or high external Pi concentrations) and a high-affinity (activated in response to Pi starvation). Here, as an initial step to understand the PHO pathway in A. fumigatus, we characterized the PHO80 homologue, phoB(PHO80). We showed that the delta phoB(PHO80) mutant has a severe polar growth defect and there is an interaction between PhoB(PHO80), calcineurin and calcium metabolism. Microarray hybridizations carried out with RNA obtained from wild type and delta phoB(PHO80) mutant cells showed that Afu4g03610 [phoD(PHO84)], Afu7g06350 [phoE9(PHO89)], Afu4g06020 [phoCPHO81)], and Afu2g09040 (vacuolar transporter Vtc4) were more expressed either in the delta phoB(PHO80) mutant background or in 11 mM Pi. Keywords: gene expression array-based (log2 ratio)

2007-11-09 | GSE9550 | GEO

Ddp1 cooperates with Ppx1 to counter a stress response initiated by non-vacuolar polyphosphate

Project description:In diverse cells from bacterial to mammalian species, inorganic phosphate is stored in long chains called polyphosphates (polyP). These near universal polymers, ranging from 3 to thousands of phosphate moieties in length, are associated with molecular functions including energy homeostasis, protein folding, and cell signaling. In many cell types, polyphosphate is concentrated in subcellular compartments or organelles. In the budding yeast S. cerevisiae, polyP synthesis by the membrane-bound VTC complex is coupled to its translocation into the lumen of the vacuole, a lysosome-related organelle, where it is stored at high concentrations. In contrast, ectopic expression of bacterial polyphosphate kinase, PPK, results in the toxic accumulation of polyP outside of the vacuole. In this study, we used label-free mass spectrometry to investigate the mechanisms underlying this toxicity. We find that PPK expression results in the activation of a stress response mediated in part by the Hog1 and Yak1 kinases, and Msn2/Msn4 transcription factors. This response is countered by the combined action of the Ddp1 and Ppx1 polyphosphatases that function together to counter polyP accumulation and downstream toxicity. In contrast, ectopic expression of previously proposed mammalian polyphosphatases did not impact PPK-mediated toxicity in the yeast model, suggesting either that these enzymes do not function directly as polyphosphatases in vivo or that they require co-factors unique to higher eukaryotes. Our work provides a mechanistic explanation for why polyP accumulation outside of lysosome-related organelles is toxic. Further, it serves as a resource for exploring how polyP may impact conserved biological processes at a molecular level.

2022-02-04 | PXD031326 | Pride

Systems analysis of phosphate-limitation induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides

Project description:Lipid accumulation by oleaginous microorganisms is of great scientific interest and biotechnological potential. While nitrogen limitation has been routinely employed, low-cost raw materials usually contain rich nitrogenous components, thus preventing from efficient lipid production. Inorganic phosphate (Pi) limitation has been found sufficient to promote conversion of sugars into lipids, yet the molecular basis of cellular response to Pi-limitation and concurrent lipid accumulation remains elusive. Here we performed multi-omic analyses of the oleaginous yeast Rhodosporidium toruloides to shield lights on Pi-limitation induced lipid accumulation. Samples were prepared under Pi-limited as well as Pi-replete chemostat conditions, and subjected to analysis at the transcriptomic, proteomic and metabolomic level. In total, 7970 genes, 4212 proteins and 123 metabolites were identified. Results showed that Pi-limitation facilitates up-regulation of Pi-associated metabolism, RNA degradation and triacylglycerol biosynthesis, while down-regulation of ribosome biosynthesis and tricarboxylic acid cycle. Pi-limitation leads to de-phosphorylation of adenosine monophosphate, the allosteric activator of isocitrate dehydrogenase key to lipid biosynthesis. It was found that NADPH, the key cofactor for fatty acid biosynthesis, is limited due to reduced flux through the pentose phosphate pathway and transhydrogenation cycle, and that this can be overcomed by overexpression of an endogenous malic enzyme. These phenomena are found distinctive from those under nitrogen-limitation. The information greatly enriches our understanding on microbial oleaginicity and Pi-related metabolism. Importantly, systems data may facilitate designing advanced cell factories for production of lipids and related oleochemicals.

2018-05-31 | GSE113097 | GEO

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