Figure 1.
Circular presentation of the S. parasanguinis FW213 chromosome.
The genome position scaled in kb from base 1 is shown on the outer circle. The second and third circles show the coding sequences on the plus and minus strands, respectively. All genes are color-coded based on the COG functional category as follows: cyan, information storage and processing; yellow, cellular processes and signaling; magenta, metabolism; black, poorly characterized. The fourth circle shows rRNA in cobalt blue and tRNA in brown. The fifth circle shows GC content (in 1-kb windows). The values that are greater than and below the average (41.62%) are in green and red, respectively. The sixth circle shows GC skew curve (10-kb window and 1-kb incremental shift). The values for plus and minus strands are shown in cobalt blue and purple, respectively. The relative locations and sizes of the five putative pathogenic islands are shown outside the scale.
Table 1.
General features of S. parasanguinis FW213 genome.
Figure 2.
The global transcriptomes of S. parasanguinis at OD 600 = 0.3 and OD 600 = 0.8.
(A) The expression levels of the sense and anti-sense strands are present at single-nt resolution in black and grey, respectively. The coverage is calculated as log(the number of reads+1)/log(1.1). (B) The numbers of genes differentially expressed under the two growth conditions according to COG classification.
Figure 3.
Determination of the transcription initiation site of Spaf_0344.
The primer extension analysis of Spaf_0344 is shown on the left side of the figure. The nucleotide sequence of the 5′ flanking region and the read counts at each nucleotide are shown on the right side of the figure. The primer extension analysis was performed with the total cellular RNA of S. parasanguinis FW213and a primer located 116-base 3′ to the ATG and containing the antisense sequence of Spaf_0344. The extended product was analyzed alongside a DNA-sequencing reaction by using the same primer. The location of the ATG start site of orf344 and the transcription initiation site (TSS) are indicated.
Figure 4.
Identification of operons based on the expression profiles.
The sequence coverage from 753,521 to 767,556 bp of the S. parasanguinis FW213 chromosome is shown. The operon is defined based on continuous expression and sequence coverage change, and the limits of the operon (Spaf_0735-Spaf_0738) are indicated by vertical arrows. The tag number of each gene is listed below the arrows. The ORFs are color-coded as described in Fig. 1 legend. The coverage is calculated as described in Fig. 2 legend.
Figure 5.
The whole genome comparison between S. parasanguinis strains.
Venn diagram representation of unique and shared gene numbers between and among strains FW213, ATCC15912, F0405 and SK236.
Figure 6.
ACT visualization of the whole genome comparison based on BLAST between strains FW213 and ATCC15912.
The red and blue bars represent the forward and reverse matches, respectively.
Table 2.
Properties of the genomic islands in S. parasanguinis FW213.
Figure 7.
Schematic representation of the putative GIs and their expression in S. parasanguinis FW213.
(A), FW213island_1; (B), FW213island_2; (C), FW213island_3; (D), FW213island_4; (E), FW213island_5. The expression levels in cultures at OD 600 = 0.3 and OD 600 = 0.8 are present at single-nt resolution in red and green, respectively. The relative sizes, locations, and orientations of the ORFs are indicated by color-coded horizontal arrows as described in Fig. 1 legend with the exception that genes of the cellular processes and signaling category are in sienna.
Table 3.
Potential virulence factors for the early exponential growth phase in S. parasanguinis FW213.
Table 4.
Potential virulence factors that are up-regulated in the early stationary phase in S. parasanguinis FW213.
Table 5.
Additional virulence factors.