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1.
Figure 3

Figure 3. Map of S. pneumoniae genomes [8]–[44], [45] and the unfinished S. mitis genome (JCVI CMR) in the area that includes the IgA1 protease gene (iga).. From: Evolution of Streptococcus pneumoniae and Its Close Commensal Relatives.

The map shows synteny apart from the absent iga gene in S. mitis NCTC 12261, in agreement with its lack of IgA1 protease activity, and apart from an additional iga paralog (zmpD) in some pneumococcus strains (INV200 and 23F) and in two strains of S. mitis [46].

Mogens Kilian, et al. PLoS ONE. 2008;3(7):e2683.
2.
Figure 2

Figure 2. Examples of long range PCR for detection of virulence genes.. From: Evolution of Streptococcus pneumoniae and Its Close Commensal Relatives.

Lane 1, molecular weight marker (sizes in kb are shown to the left); lanes 2–6, S. pneumoniae strains TIGR4, SK848, SK851, SK856, and SK858; lanes 7 and 8, S. pseudopneumoniae strains SK1069 and SK674; lanes 9–12, S. mitis strains SK575, SK568, SK142, and T2186; lanes 13 and 14, S. oralis strains SK23 and SK141. (A) PCR with primers aliA and dexB flanking the cap gene cluster. Amplicons larger than 7 kb represent the area between the genes aliA and dexB, whereas partial sequencing and control PCRs revealed that the smaller ones in lanes 7–13 are artifacts due to amplification of different regions with the aliA primer alone. The S. pseudopneumoniae, S. mitis, and S. oralis strains were selected to illustrate these artifacts. (B) and (C) Amplicons resulting from PCR with primers flanking the ply-lytA region and the iga gene, respectively.

Mogens Kilian, et al. PLoS ONE. 2008;3(7):e2683.
3.
Figure 1

Figure 1. Phylogenetic tree constructed with the minimum evolution algorithm in MEGA version 4.0 and based on concatenated partial sequences of the house-keeping enzyme genes ddl, gdh, rpoB, and sodA.. From: Evolution of Streptococcus pneumoniae and Its Close Commensal Relatives.

Type strains of individual species are shown with species designation. Bootstrap values (%) are based on 1000 replications. The three major clusters supported by significant bootstrap values are the pneumoniae-mitis-pseudopneumoniae cluster (red lines), the Oralis cluster (blue lines), and the Infantis cluster (green lines). The subcluster of S. pneumoniae strains within the pneumoniae-mitis-pseudopneumoniae cluster is indicated by dark red lines (ruby), S. pseudoneumoniae strains within the pneumoniae-mitis-pseudopneumoniae cluster are indicated by pink, and strains previously assigned to “S. mitis biovar 2” within the Oralis cluster are indicated by dark blue lines. The random presence of homologues of virulence factors usually associated with S. pneumoniae (cap locus, capsule synthesis operon; iga, IgA1 protease gene; lytA, autolysin gene; ply, pneumolysin gene) in the diverse population of Mitis lineages is illustrated. A red signature indicates presence of the virulence gene, and black signature indicates a PCR product size compatible with absence of the gene. Black squares with a red center indicate IgA1 protease activity but an amplicon size in support of lack of an iga gene in the context found in S. pneumoniae. No signature indicates lack of a PCR product presumably due to no match of the primers. The arrow indicates the hypothetical immediate common ancestor of the red cluster. The scale bar refers to genetic divergence as calculated by the MEGA software.

Mogens Kilian, et al. PLoS ONE. 2008;3(7):e2683.

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