B. mori Host Response to Bb Figure 3. Differentially regulated genes during Bb infection. (a) Clustered expression profiles of regulated 2436 genes taken 2.0-fold cutoff criterion from 3 h to 24 h. For expanded ratios and annotation details, see Table S2. (b) Mean expression values of genes (log2) located in the defined clusters. doi:10.1371/journal.pone.0008098.g003 N, eukaryotic Pol III C25, eukaryotic Pol II B6, eukaryotic Pol III C5, eukaryotic Pol II B3 and eukaryotic Pol II B5. Similarly, basic transcription factors were also induced by Bb infection, including TFIID11, TFIID1, TFIIA1, TFIIE2 and TFIID10. Only TFIID1 was downregulated, and the other five genes were upregulated. These data indicated that the synthesis of nucleic acids and proteins was increased after infection. The basic genetic information processing and transcription genes upregulation Figure 2. General statistics on the genes regulated after Bb oral infection. (a) The number of up- and down-regulated genes after Bb oral infection at 3 h, 6 h, 12 h and 24 h time points (h: hours post infection). (b) GO categories of total Bb oral induced genes. doi:10.1371/journal.pone.0008098.g002 68 were midgut tissue-specific; these 68 accounted for 30.56% of all the midgut specific genes, the highest level for all tissues (Fig. 4b). Many of the induced midgut genes encode metalloproteinases, hydrolases, lipases and chitin structural proteins. The midgut, as the direct infection organ, showed a relatively high level of tissue-specific gene expression. Basal Metabolic Pathways Involved after Bb Infection The basic metabolism is important for organisms to maintain their normal physiological activities. Analysis of pathogen-induced host basal metabolic pathways will help us to investigate the interaction between them. Using the significant standard criteria of pathway prediction value P,0.05 and induced ratios.2 or ,0.5, we searched the KEGG database to filter out the host metabolic pathway-related genes [29–33]. In total, six types of basal metabolic systems were identified after the infection, including genetic information processing and transcription, nucleic acid metabolism, metabolism of cofactors and vitamins, xenobiotics biodegradation and metabolism, amino acid metabolism and nitrogen metabolism, and carbohydrate metabolism (Fig. 5). These pathways are involved in many normal silkworm physiological metabolic processes. The detailed enzyme names, gene IDs, KEGG prediction P-values and their typical catalytic reactions are shown in Table S1, and the ratios of the pathway groups are shown in Table S4. Basic genetic information processing and transcription genes. Nucleotide biosynthesis is critical for growth of bacteria in human blood [34]. For the silkworm, both the maintenance of normal growth and development for itself and proliferation of bacteria in its hemolymph need nucleotide acids for the transmission of genetic information and protein synthesis. As a result, the genes encoding RNA polymerases and basic transcription factors were modulated (Fig. 5). Nine RNA polymerases were upregulated at 24 hpi, including eukaryotic Pol II B4, eukaryotic Pol I A12, eukaryotic Pol III C11, archaeal PLoS ONE | www.plosone.org 4 December 2009 | Volume 4 | Issue 12 | e8098