Analysis of temporal gene regulation of Listeria monocytogenes revealed distinct regulatory response modes after exposure to high pressure processing

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Nikparvar , B , Andreevskaya , M , Duru , I C , Bucur , F I , Grigore-Gurgu , L , Borda , D , Nicolau , A I , Riedel , C U , Auvinen , P & Bar , N 2021 , ' Analysis of temporal gene regulation of Listeria monocytogenes revealed distinct regulatory response modes after exposure to high pressure processing ' , BMC Genomics , vol. 22 , no. 1 , 266 . https://doi.org/10.1186/s12864-021-07461-0

Title: Analysis of temporal gene regulation of Listeria monocytogenes revealed distinct regulatory response modes after exposure to high pressure processing
Author: Nikparvar, Bahareh; Andreevskaya, Margarita; Duru, Ilhan C.; Bucur, Florentina I.; Grigore-Gurgu, Leontina; Borda, Daniela; Nicolau, Anca I.; Riedel, Christian U.; Auvinen, Petri; Bar, Nadav
Contributor: University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
Date: 2021-04-14
Language: eng
Number of pages: 15
Belongs to series: BMC Genomics
ISSN: 1471-2164
URI: http://hdl.handle.net/10138/330319
Abstract: Background The pathogen Listeria (L.) monocytogenes is known to survive heat, cold, high pressure, and other extreme conditions. Although the response of this pathogen to pH, osmotic, temperature, and oxidative stress has been studied extensively, its reaction to the stress produced by high pressure processing HPP (which is a preservation method in the food industry), and the activated gene regulatory network (GRN) in response to this stress is still largely unknown. Results We used RNA sequencing transcriptome data of L. monocytogenes (ScottA) treated at 400 MPa and 8(circle)C, for 8 min and combined it with current information in the literature to create a transcriptional regulation database, depicting the relationship between transcription factors (TFs) and their target genes (TGs) in L. monocytogenes. We then applied network component analysis (NCA), a matrix decomposition method, to reconstruct the activities of the TFs over time. According to our findings, L. monocytogenes responded to the stress applied during HPP by three statistically different gene regulation modes: survival mode during the first 10 min post-treatment, repair mode during 1 h post-treatment, and re-growth mode beyond 6 h after HPP. We identified the TFs and their TGs that were responsible for each of the modes. We developed a plausible model that could explain the regulatory mechanism that L. monocytogenes activated through the well-studied CIRCE operon via the regulator HrcA during the survival mode. Conclusions Our findings suggest that the timely activation of TFs associated with an immediate stress response, followed by the expression of genes for repair purposes, and then re-growth and metabolism, could be a strategy of L. monocytogenes to survive and recover extreme HPP conditions. We believe that our results give a better understanding of L. monocytogenes behavior after exposure to high pressure that may lead to the design of a specific knock-out process to target the genes or mechanisms. The results can help the food industry select appropriate HPP conditions to prevent L. monocytogenes recovery during food storage.
Subject: Gene regulatory network
Listeria monocytogenes
High pressure processing
Network component analysis
Transcription factor
Target gene
HEAT-SHOCK RESPONSE
SIGNAL-TRANSDUCTION SYSTEM
NETWORK COMPONENT ANALYSIS
ENVELOPE STRESS-RESPONSE
ESCHERICHIA-COLI
MEMBRANE DAMAGE
EXPRESSION
HRCA
TRANSCRIPTOME
INACTIVATION
1184 Genetics, developmental biology, physiology
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