title: Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium.
abstract: BACKGROUND
  Global patterns of gene expression of Escherichia coli K-12 during growth transitions have been deeply investigated, however, comparable studies of E. coli O157:H7 have not been explored, particularly with respect to factors regulating virulence genes and genomic islands specific to this pathogen. To examine the impact of growth phase on the dynamics of the transcriptome, O157:H7 Sakai strain was cultured in MOPS minimal media (0.1% glucose), RNA harvested at 10 time points from early exponential to full stationary phase, and relative gene expression was measured by co-hybridization on high-density DNA microarrays. Expression levels of 14 genes, including those encoding Shiga toxins and other virulence factors associated with the locus of enterocyte effacement (LEE), were confirmed by Q-PCR.
  
  
  RESULTS
  Analysis of variance (R/MAANOVA, Fs test) identified 442 (36%) of 1239 O157-specific ORFs and 2110 (59%) of 3647 backbone ORFs that changed in expression significantly over time. QT cluster analysis placed 2468 of the 2552 significant ORFs into 12 groups; each group representing a distinct expression pattern. ORFs from the largest cluster (n = 1078) decreased in expression from late exponential to early stationary phase: most of these ORFs are involved in functions associated with steady state growth. Also represented in this cluster are ORFs of the TAI island, encoding tellurite resistance and urease activity, which decreased approximately 4-fold. Most ORFs of the LEE pathogenicity island also decreased approximately 2-fold by early stationary phase. The ORFs encoding proteins secreted via the LEE encoded type III secretion system, such as tccP and espJ, also decreased in expression from exponential to stationary phase. Three of the clusters (n = 154) comprised genes that are transiently upregulated at the transition into stationary phase and included genes involved in nutrient scavenging. Upregulated genes with an increase in mRNA levels from late exponential to early stationary phase belonged to one cluster (n = 923) which includes genes involved in stress responses (e.g. gadAB, osmBC, and dps). These transcript levels remained relatively high for > 3 h in stationary phase. The Shiga toxin genes (stx1AB and stx2B) were significantly induced after transition into stationary phase.
  
  
  CONCLUSIONS
  Expression of more than 300 O157-specific ORFs, many implicated in virulence of the O157 pathogen, was modulated in a growth dependent manner. These results provide a baseline transcriptional profile that can be compared to patterns of gene expression of this important foodborne pathogen under adverse environmental conditions.
authors.affiliation: Microbial Evolution Laboratory, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, USA. largeter@msu.edu
authors.forename: Teresa M
authors.initials: TM
authors.lastname: Bergholz
authors.forename: Lukas M
authors.initials: LM
authors.lastname: Wick
authors.forename: Weihong
authors.initials: W
authors.lastname: Qi
authors.forename: James T
authors.initials: JT
authors.lastname: Riordan
authors.forename: Lindsey M
authors.initials: LM
authors.lastname: Ouellette
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Whittam
mesh_terms: D000704:Analysis of Variance; D016000:Cluster Analysis; D003470:Culture Media; D019453:Escherichia coli O157 / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D015964:Gene Expression Regulation, Bacterial; D044404:Genomic Islands; D005947:Glucose / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D010100:Oxygen / Q000378:metabolism; D022621:Shiga Toxin / Q000235:genetics / Q000378:metabolism; D037521:Virulence Factors / Q000378:metabolism
chemical_list: D003470:Culture Media; D037521:Virulence Factors; D022621:Shiga Toxin; D005947:Glucose; D010100:Oxygen