Open Access Research article

Non-essential genes form the hubs of genome scale protein function and environmental gene expression networks in Salmonella enterica serovar Typhimurium

Jesper T Rosenkrantz1, Henk Aarts2, Tjakko Abee3, Matthew D Rolfe4, Gitte M Knudsen45, Maj-Britt Nielsen16, Line E Thomsen1, Marcel H Zwietering3, John E Olsen1* and Carmen Pin4

Author Affiliations

1 Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, C, Denmark

2 Centre for Infectious disease control, National Institute for Public Health, PO box 1, 3720 BA Bilthoven, The Netherlands

3 Wageningen University and Research Centre, Laboratory of Food Microbiology, P.O. Box 17, 6700 AA Wageningen, Netherlands

4 Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK

5 National Food Institute, Danish Technical University, Soelvtofts Plads, 2800 Kgs. Lyngby, Denmark

6 Present address: DANSTEM Laboratory, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, N, Denmark

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BMC Microbiology 2013, 13:294  doi:10.1186/1471-2180-13-294

Published: 17 December 2013

Abstract

Background

Salmonella Typhimurium is an important pathogen of human and animals. It shows a broad growth range and survives in harsh conditions. The aim of this study was to analyze transcriptional responses to a number of growth and stress conditions as well as the relationship of metabolic pathways and/or cell functions at the genome-scale-level by network analysis, and further to explore whether highly connected genes (hubs) in these networks were essential for growth, stress adaptation and virulence.

Results

De novo generated as well as published transcriptional data for 425 selected genes under a number of growth and stress conditions were used to construct a bipartite network connecting culture conditions and significantly regulated genes (transcriptional network). Also, a genome scale network was constructed for strain LT2. The latter connected genes with metabolic pathways and cellular functions. Both networks were shown to belong to the family of scale-free networks characterized by the presence of highly connected nodes or hubs which are genes whose transcription is regulated when responding to many of the assayed culture conditions or genes encoding products involved in a high number of metabolic pathways and cell functions.

The five genes with most connections in the transcriptional network (wraB, ygaU, uspA, cbpA and osmC) and in the genome scale network (ychN, siiF (STM4262), yajD, ybeB and dcoC) were selected for mutations, however mutagenesis of ygaU and ybeB proved unsuccessful. No difference between mutants and the wild type strain was observed during growth at unfavorable temperatures, pH values, NaCl concentrations and in the presence of H2O2. Eight mutants were evaluated for virulence in C57/BL6 mice and none differed from the wild type strain. Notably, however, deviations of phenotypes with respect to the wild type were observed when combinations of these genes were deleted.

Conclusion

Network analysis revealed the presence of hubs in both transcriptional and functional networks of S. Typhimurium. Hubs theoretically confer higher resistance to random mutation but a greater susceptibility to directed attacks, however, we found that genes that formed hubs were dispensable for growth, stress adaptation and virulence, suggesting that evolution favors non-essential genes as main connectors in cellular networks.