Dataset Information

Resuscitation from the viable but nonculturable state of Escherichia coli: the importance of a pyruvate sensing network

ABSTRACT: Viable but nonculturable (VBNC) organisms have been underestimated and neglected when studying dormant phenotypes. In clinical settings, VBNC cells may contribute to non-apparent infections capable of being reactivated after months or even years, as for the case of Mycobacterium tuberculosis. The lack of specific and reliable methodology prevents the proper characterization of the VBNC state. Ultimately, these organisms pose a public health risk with potential implications in several industries ranging from pharmaceuticals to food industry. Research regarding their induction and resuscitation is of major importance. Bacteria are able to respond to several environmental and physiological oscillations in part via two-component systems (TCSs). BtsS/BtsR and YpdA/YpdB are two TCSs of Escherichia coli that form a pyruvate sensing network. Their role in the VBNC state is explored in this study.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli

SUBMITTER: Ignasi Forne

LAB HEAD: Prof. Dr. Kirsten Jung

PROVIDER: PXD009463 | Pride | 2018-11-23

REPOSITORIES: Pride

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Publications

Importance of Pyruvate Sensing and Transport for the Resuscitation of Viable but Nonculturable Escherichia coli K-12.

Vilhena Cláudia C Kaganovitch Eugen E Grünberger Alexander A Motz Magdalena M Forné Ignasi I Kohlheyer Dietrich D Jung Kirsten K

Journal of bacteriology 20190111 3

Escherichia coli and many other bacterial species can enter into a viable but nonculturable (VBNC) state, which is a survival strategy adopted by cells exposed to adverse environmental conditions. Pyruvate is known to be one factor that promotes resuscitation of VBNC cells. Here we studied the role of a pyruvate-sensing network, composed of the histidine kinase-response regulator systems BtsS/BtsR and YpdA/YpdB and the target gene btsT, encoding the high-affinity pyruvate/H+</ ...[more]

PMID: 30420452

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Project description:For assessing the cancer-causing potential for humans of a chemical compound, the conventional approach is the use of the 2-year rodent carcinogenicity bioassay, thus alternatives such as in vitro toxicogenomics are highly desired. In the present study, the transcriptomics responses following exposure to genotoxic (GTX) and non-genotoxic (NGTX) hepatocarcinogens and non-carcinogens (NC) in five liver-based in vitro models, namely conventional and epigenetically-stabilized cultures of primary rat hepatocytes, the human hepatoma-derived HepaRG and HepG2 cell lines and the human embryonic stem cell-derived hepatocyte-like cells hES-Heps are examined and compared. The global gene expression profiles of five commonly used liver-based in vitro systems are investigated, namely conventional cultures of primary rat hepatocytes (HepsC), Trichostatin A (TSA)-stabilized cultures of primary rat hepatocytes (HepsT), human embryonic stem cell-derived hepatocyte-like cells (hES-Hep), HepG2 and HepaRG cells. These models are exposed to 15 prototypical compounds which have been carefully chosen and belong to 3 toxic classes i.e. (i) genotoxic (GTX) (aflatoxin B1, AFB1; 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, NNK; 2-nitrofluorene, 2NF; benzo(a)pyrene, BaP; cyclophosphamide, CYCLO), (ii) non-genotoxic (NGTX) (methapyrilene hydrochloride, MPH; piperonylbutoxide , PIPB; Wy-14643, WYE; phenobarbital sodium, SPB; 12-O-tetradecanoylphorbol-13-acetate, TPA) carcinogens and (iii) non-carcinogens (NC) (nifedipine, NIF; clonidine, CND; D-mannitol, MAN; tolbutamide, TOL; diclofenac sodium, SDF). For the gene- and pathway- based analysis, the raw microarray data was re-annotated to Ensembl version 61 genome and Gene Chip Robust Multi-array Average (GC-RMA) normalized (Dai et al. 2005). This resulted in 11,187 and 18,919 probe sets for the rat and the human models, respectively. For the classification analysis, the raw microarray data was annotated using the chip description files from Affymetrix and then GC-RMA normalized. In order to eliminate batch effects, data from the different studies were half-z normalized. Half-z-normalization adjusts the logarithmic expression values of transcripts within a group such that each transcript has zero mean.

Dataset Information

Resuscitation from the viable but nonculturable state of Escherichia coli: the importance of a pyruvate sensing network

Publications

Importance of Pyruvate Sensing and Transport for the Resuscitation of Viable but Nonculturable <i>Escherichia coli</i> K-12.

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