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

Abstract

BackgroundSalmonella 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.ResultsDe 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.ConclusionNetwork 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.

Systematic Review of Mutations in Pyrazinamidase Associated with Pyrazinamide Resistance in Mycobacterium tuberculosis Clinical Isolates

“…In brief, since pncA is believed to be nonessential (40), mutations may confer low to no fitness cost, resulting in no selective pressure on the functional protein, which in turn can result in mutations occurring anywhere in the gene without a loss of fitness. However, it has been shown previously that although a gene may be considered nonessential in vitro, it may be essential in vivo (87,88). From the protein science point of view, it is difficult to imagine how mutations scattered all over the enzyme and away from the active site can render the enzyme dysfunctional.…”

Gene co-expression analysis for functional classification and gene–disease predictions

“…One study using myocardial data from 1617 samples found that known foetal gene markers upregulated in gene networks common to developing and diseased myocardium were not hub genes [ 79 ]. Another co-expression study in Salmonella found that hub genes are dispensable for growth, stress adaptation and virulence, suggesting that hub genes are not necessarily essential [ 80 ].…”

Salmonella—how a metabolic generalist adopts an intracellular lifestyle during infection

“…Salmonella , like several other Gamma-proteobacteria, are found in various environments including soils, water systems, and sewage, as well as in the gut flora of various animals. To survive and multiply in this large variety of environments, their metabolism has to adapt well (Rosenkrantz et al, 2013 ). The large genome of Salmonella contains more than 4000 genes encoding a large range of metabolic pathways, for instance an S .…”

“…Rosenkrantz et al ( 2013 ) compared two types of networks for S . Typhimurium strain LT2 regarding stress response and metabolic adaptation: a transcriptional data network using transcriptional data for 425 selected genes under different growth and stress conditions identifying the significantly and strongly regulated genes (transcriptional network) for each condition.…”

“…Looking at the top five connecting hub proteins from the transcriptional network ( wraB, ygaU, uspA, cbpA, and osmC ) as well as the hubs in the genome scale metabolic pathway and cellular function network ( ychN, siiF, yajD, ybeB, and dcoC ), all these hubs were found to be dispensable for virulence in mutation studies. However, double mutants of these two sets of regulatory proteins showed clear effects on virulence in mouse infection experiments (Rosenkrantz et al, 2013 ). This is a particular strong example confirming the robust and well-buffered Salmonella regulation of metabolism and cellular function with virulence factors having partly redundant, overlapping functions.…”