Limits...
Insight into the specific virulence related genes and toxin-antitoxin virulent pathogenicity islands in swine streptococcosis pathogen Streptococcus equi ssp. zooepidemicus strain ATCC35246.

Ma Z, Geng J, Yi L, Xu B, Jia R, Li Y, Meng Q, Fan H, Hu S - BMC Genomics (2013)

Bottom Line: Analysis of the genome identified potential Sz35246 virulence genes.Genes of the Fim III operon were presumed to be involved in breaking the host-restriction of Sz35246.Genome wide comparisons of Sz35246 with three other strains and transcriptome analysis revealed novel genes related to bacterial virulence and breaking the host-restriction.

View Article: PubMed Central - HTML - PubMed

Affiliation: College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.

ABSTRACT

Background: Streptococcus equi ssp. zooepidemicus (S. zooepidemicus) is an important pathogen causing swine streptococcosis in China. Pathogenicity islands (PAIs) of S. zooepidemicus have been transferred among bacteria through horizontal gene transfer (HGT) and play important roles in the adaptation and increased virulence of S. zooepidemicus. The present study used comparative genomics to examine the different pathogenicities of S. zooepidemicus.

Results: Genome of S. zooepidemicus ATCC35246 (Sz35246) comprises 2,167,264-bp of a single circular chromosome, with a GC content of 41.65%. Comparative genome analysis of Sz35246, S. zooepidemicus MGCS10565 (Sz10565), Streptococcus equi. ssp. equi. 4047 (Se4047) and S. zooepidemicus H70 (Sz70) identified 320 Sz35246-specific genes, clustered into three toxin-antitoxin (TA) systems PAIs and one restriction modification system (RM system) PAI. These four acquired PAIs encode proteins that may contribute to the overall pathogenic capacity and fitness of this bacterium to adapt to different hosts. Analysis of the in vivo and in vitro transcriptomes of this bacterium revealed differentially expressed PAI genes and non-PAI genes, suggesting that Sz35246 possess mechanisms for infecting animals and adapting to a wide range of host environments. Analysis of the genome identified potential Sz35246 virulence genes. Genes of the Fim III operon were presumed to be involved in breaking the host-restriction of Sz35246.

Conclusion: Genome wide comparisons of Sz35246 with three other strains and transcriptome analysis revealed novel genes related to bacterial virulence and breaking the host-restriction. Four specific PAIs, which were judged to have been transferred into Sz35246 genome through HGT, were identified for the first time. Further analysis of the TA and RM systems in the PAIs will improve our understanding of the pathogenicity of this bacterium and could lead to the development of diagnostics and vaccines.

Show MeSH

Related in: MedlinePlus

Circular representation of the S. zoopedemicus ATCC35246 genome and comparative genome results. The ten circles (outer to inner) show the following. The outer three circles represent Sz35246 protein-encoding genes homologous to that of Sz10565, Sz70 and Se4047, respectively. The fourth circle represents the PAI in Sz35246 chromosome. The fifth circle shows the chromosome position scaled in kb from oriC. The sixth and seventh circles show the coding sequences on the plus and minus strands, respectively. All genes are color-coded based on the COG functional categories: cyan, information storage and processing; yellow, cellular processes and signaling; magenta, metabolism; and black, poorly characterized. The eighth circle shows rRNA in red and tRNA in blue. The ninth circle shows the GC content (in 1-kb windows).Values that are greater than and or less than the average (41.65%) are shown in green and red, respectively. The tenth circle shows the 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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3750634&req=5

Figure 1: Circular representation of the S. zoopedemicus ATCC35246 genome and comparative genome results. The ten circles (outer to inner) show the following. The outer three circles represent Sz35246 protein-encoding genes homologous to that of Sz10565, Sz70 and Se4047, respectively. The fourth circle represents the PAI in Sz35246 chromosome. The fifth circle shows the chromosome position scaled in kb from oriC. The sixth and seventh circles show the coding sequences on the plus and minus strands, respectively. All genes are color-coded based on the COG functional categories: cyan, information storage and processing; yellow, cellular processes and signaling; magenta, metabolism; and black, poorly characterized. The eighth circle shows rRNA in red and tRNA in blue. The ninth circle shows the GC content (in 1-kb windows).Values that are greater than and or less than the average (41.65%) are shown in green and red, respectively. The tenth circle shows the 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.

Mentions: The 2,167,264-bp genome of Sz35246 comprises a single circular chromosome with a GC content of 41.65% (Additional file1: Table S1 & FigureĀ 1) and the genome information have been reported previously[11]. The GC content is similar to that of Streptococcus equi subsp. zooepidemicus MGCS10565 (Sz10565)[12], Streptococcus equi subsp. equi 4047 (Se4047) and Streptococcus equi subsp. zooepidemicus H70 (Sz70)[13]. The genome contains 2,087 protein-encoding genes, 57 tRNA genes, and five 5S-16S-23S rRNA operon gene clusters. Among the protein coding genes, 416 (19.93%) are predicted to encode conserved hypothetical proteins that are similar to proteins of unknown factions in other genomes, and 137 hypothetical genes (6.56%) have no matches in the nr protein database (Additional file1: Table S1). The remaining 1534 genes were assigned putative functions. Eighty-one genes were identified as mobile elements, including those encoding a competence protein, a phage associated protein, a conjugation protein, a transposase and a site-specific recombinase, suggesting that these elements are used to take up and incorporate foreign DNA and are involved in reconstructing the genome architecture. Furthermore, global transcriptome analysis of Sz35246 using RNA-seq confirmed that 2048 of the 2,087 ORFs are expressed, but with different sequence coverages in vitro and in vivo (Additional file1: Table S1). Comparative gene expression analysis reveals that 252 genes are upregulated and 142 genes are downregulated (Additional file2: Table S2) by more than a 2-fold change in reads per kilo base per million (RPKM) values (p < 0.001) in vivo. The upregulated genes include 67 hypothetical protein coding genes and 28 response regulator, transcription regulator genes and chaperone protein encoding genes, suggesting that the differential expression of these ORFs plays an important role in survival of Sz35246 within the different host environments.


Insight into the specific virulence related genes and toxin-antitoxin virulent pathogenicity islands in swine streptococcosis pathogen Streptococcus equi ssp. zooepidemicus strain ATCC35246.

Ma Z, Geng J, Yi L, Xu B, Jia R, Li Y, Meng Q, Fan H, Hu S - BMC Genomics (2013)

Circular representation of the S. zoopedemicus ATCC35246 genome and comparative genome results. The ten circles (outer to inner) show the following. The outer three circles represent Sz35246 protein-encoding genes homologous to that of Sz10565, Sz70 and Se4047, respectively. The fourth circle represents the PAI in Sz35246 chromosome. The fifth circle shows the chromosome position scaled in kb from oriC. The sixth and seventh circles show the coding sequences on the plus and minus strands, respectively. All genes are color-coded based on the COG functional categories: cyan, information storage and processing; yellow, cellular processes and signaling; magenta, metabolism; and black, poorly characterized. The eighth circle shows rRNA in red and tRNA in blue. The ninth circle shows the GC content (in 1-kb windows).Values that are greater than and or less than the average (41.65%) are shown in green and red, respectively. The tenth circle shows the 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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750634&req=5

Figure 1: Circular representation of the S. zoopedemicus ATCC35246 genome and comparative genome results. The ten circles (outer to inner) show the following. The outer three circles represent Sz35246 protein-encoding genes homologous to that of Sz10565, Sz70 and Se4047, respectively. The fourth circle represents the PAI in Sz35246 chromosome. The fifth circle shows the chromosome position scaled in kb from oriC. The sixth and seventh circles show the coding sequences on the plus and minus strands, respectively. All genes are color-coded based on the COG functional categories: cyan, information storage and processing; yellow, cellular processes and signaling; magenta, metabolism; and black, poorly characterized. The eighth circle shows rRNA in red and tRNA in blue. The ninth circle shows the GC content (in 1-kb windows).Values that are greater than and or less than the average (41.65%) are shown in green and red, respectively. The tenth circle shows the 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.
Mentions: The 2,167,264-bp genome of Sz35246 comprises a single circular chromosome with a GC content of 41.65% (Additional file1: Table S1 & FigureĀ 1) and the genome information have been reported previously[11]. The GC content is similar to that of Streptococcus equi subsp. zooepidemicus MGCS10565 (Sz10565)[12], Streptococcus equi subsp. equi 4047 (Se4047) and Streptococcus equi subsp. zooepidemicus H70 (Sz70)[13]. The genome contains 2,087 protein-encoding genes, 57 tRNA genes, and five 5S-16S-23S rRNA operon gene clusters. Among the protein coding genes, 416 (19.93%) are predicted to encode conserved hypothetical proteins that are similar to proteins of unknown factions in other genomes, and 137 hypothetical genes (6.56%) have no matches in the nr protein database (Additional file1: Table S1). The remaining 1534 genes were assigned putative functions. Eighty-one genes were identified as mobile elements, including those encoding a competence protein, a phage associated protein, a conjugation protein, a transposase and a site-specific recombinase, suggesting that these elements are used to take up and incorporate foreign DNA and are involved in reconstructing the genome architecture. Furthermore, global transcriptome analysis of Sz35246 using RNA-seq confirmed that 2048 of the 2,087 ORFs are expressed, but with different sequence coverages in vitro and in vivo (Additional file1: Table S1). Comparative gene expression analysis reveals that 252 genes are upregulated and 142 genes are downregulated (Additional file2: Table S2) by more than a 2-fold change in reads per kilo base per million (RPKM) values (p < 0.001) in vivo. The upregulated genes include 67 hypothetical protein coding genes and 28 response regulator, transcription regulator genes and chaperone protein encoding genes, suggesting that the differential expression of these ORFs plays an important role in survival of Sz35246 within the different host environments.

Bottom Line: Analysis of the genome identified potential Sz35246 virulence genes.Genes of the Fim III operon were presumed to be involved in breaking the host-restriction of Sz35246.Genome wide comparisons of Sz35246 with three other strains and transcriptome analysis revealed novel genes related to bacterial virulence and breaking the host-restriction.

View Article: PubMed Central - HTML - PubMed

Affiliation: College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.

ABSTRACT

Background: Streptococcus equi ssp. zooepidemicus (S. zooepidemicus) is an important pathogen causing swine streptococcosis in China. Pathogenicity islands (PAIs) of S. zooepidemicus have been transferred among bacteria through horizontal gene transfer (HGT) and play important roles in the adaptation and increased virulence of S. zooepidemicus. The present study used comparative genomics to examine the different pathogenicities of S. zooepidemicus.

Results: Genome of S. zooepidemicus ATCC35246 (Sz35246) comprises 2,167,264-bp of a single circular chromosome, with a GC content of 41.65%. Comparative genome analysis of Sz35246, S. zooepidemicus MGCS10565 (Sz10565), Streptococcus equi. ssp. equi. 4047 (Se4047) and S. zooepidemicus H70 (Sz70) identified 320 Sz35246-specific genes, clustered into three toxin-antitoxin (TA) systems PAIs and one restriction modification system (RM system) PAI. These four acquired PAIs encode proteins that may contribute to the overall pathogenic capacity and fitness of this bacterium to adapt to different hosts. Analysis of the in vivo and in vitro transcriptomes of this bacterium revealed differentially expressed PAI genes and non-PAI genes, suggesting that Sz35246 possess mechanisms for infecting animals and adapting to a wide range of host environments. Analysis of the genome identified potential Sz35246 virulence genes. Genes of the Fim III operon were presumed to be involved in breaking the host-restriction of Sz35246.

Conclusion: Genome wide comparisons of Sz35246 with three other strains and transcriptome analysis revealed novel genes related to bacterial virulence and breaking the host-restriction. Four specific PAIs, which were judged to have been transferred into Sz35246 genome through HGT, were identified for the first time. Further analysis of the TA and RM systems in the PAIs will improve our understanding of the pathogenicity of this bacterium and could lead to the development of diagnostics and vaccines.

Show MeSH
Related in: MedlinePlus