Figure 1.
Volcano Plot of fold change versus significance.
Gene expression data for Y. intermedia grown under aerobic and anaerobic conditions was used to derive log2 ratios (X-axis) which are plotted against posterior probability of differential expression for each of the genes derived using EBarrays (Y-axis) to generate a volcano plot to visualize differential expression. Significant and insignificant genes are represented by black and grey diamonds, respectively. Red diamonds represent orthologs of genes identified as constituting the core anaerobic transcriptome of three enterobacterial members grown in the presence of glucose. A set of 20 genes were identified as likely to constitute the minimal core anaerobic transcriptome of the Enterobacteriaceae in the presence of glucose as the carbon source [22]. These 20 genes shared a 1-1-1 orthologous relationship between three members of the Enterobacteriaceae, namely E. coli K-12-MG1655, Dickeya dadantii 3937 and Pectobacterium atrosepticum SCRI1043 and for all of the 20 genes the pattern of expression was similar, the magnitude of change was greater than 3-fold and the genetic architecture was highly conserved. While the exact functions of most of these genes are established in the model organism E. coli that of few others still remain elusive. Of these 20 genes, 18 were differentially expressed and showed similar pattern of expression in Y. intermedia in this study. These are frdABCD (fumarate reductase), focA, yfiD, (pyruvate formate lyase), adhE (aldehyde dehydrogenases), ynfK (dethiobiotin synthetase), hypC (hydrogenase components), nrdD (anaerobic ribonucleotide reductase), dcuB (dicarboxylate transporter), yhbUV (collagenase-like proteins), pepT (peptidase), ycbJ (uncharacterized protein), exbB (the membrane-spanning protein of the TonB-exbBD complex), yceJ (cytochrome), yceI (uncharacterized protein). Except for five genes (yfiD, yhbV,ycbJ, yceJ, yceI), all of the remaining 13 genes showed fold changes greater than 3 (our stringent criteria established in a previous study) in Y. intermedia. The only gene which is present in the core but missing in the differentially expressed set in Y. intermedia is nrdG (anaerobically functioning ribonucleotide reductase).
Figure 2.
Graphical representation of 392 differentially expressed genes in Y. intermedia which have homologs in at least one of the pathogenic yersiniae.
Phylogenprofiler (Integrated Microbial Genomes) was used with analytical settings as described in methods to obtain homologs of Y. intermedia in other yersiniae. A Venn diagram was built to display the number of differentially expressed genes in Y. intermedia that have homologs in Y. enterocolitica (Ye8081, blue circle, 376 genes), Y. pseudotuberculosis (Ytb31758, purple circle, 319 genes) and Y. pestis (YpCO92, red circle, 299 genes).
Figure 3.
Functional categories of anaerobically up-regulated (yellow) and anaerobically down-regulated (blue) genes.
Genes from Table S1 were broadly categorized according to their biological function. Each bar represents the actual number of genes.