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Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.

Lin IH, Liu TT, Teng YT, Wu HL, Liu YM, Wu KM, Chang CH, Hsu MT - PLoS ONE (2011)

Bottom Line: We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans.This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced.The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.

View Article: PubMed Central - PubMed

Affiliation: Institute of BioMedical Informatics, National Yang-Ming University, Taipei, Taiwan.

ABSTRACT
Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection. Here, we present the complete genomes of S. gallolyticus ATCC 43143 (biotype I) and S. pasteurianus ATCC 43144 (biotype II.2). The genomic differences between the two biotypes were characterized with comparative genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length and encode 2246 and 1869 CDS respectively. The organization and genomic contents of both genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92%) and 1607 (86%) of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively. There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus genus has a small core-genome (constitute around 30% of total CDS) and substantial evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC 43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to contribute to the fitness and virulence of each of the two subspecies. We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans. This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.

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Related in: MedlinePlus

Circular representation of the S. gallolyticus ATCC 43143 and S. pasteurianus ATCC 43144 genomes.From the outside in, the outer two circles shows open reading frames oriented in the forward (red) and reverse (blue) direction, respectively. The third circle marks the rRNA gene operon (pink) and the fourth circle shows the tRNA genes (orange). The fifth circle shows GC skew, purple indicating negative values whereas olive for positive values. The inner-most circle shows the G+C% content plot.
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pone-0020519-g001: Circular representation of the S. gallolyticus ATCC 43143 and S. pasteurianus ATCC 43144 genomes.From the outside in, the outer two circles shows open reading frames oriented in the forward (red) and reverse (blue) direction, respectively. The third circle marks the rRNA gene operon (pink) and the fourth circle shows the tRNA genes (orange). The fifth circle shows GC skew, purple indicating negative values whereas olive for positive values. The inner-most circle shows the G+C% content plot.

Mentions: The genome of S. gallolyticus ATCC 43143 and S. pasteurianus ATCC 43144 each comprises a single circular chromosome of 2,362,241 bp and 2,100,077 bp respectively (Figure 1). The general features are presented in Table 1. The average G+C contents of both genomes are 37% and neither contains any plasmids. There are 61 tRNA genes and five rRNA operons in each chromosomes, with most of the tRNA genes situated close to rRNA operons. A total of 2246 protein-coding genes are predicted in ATCC 43143, much similar to the recently sequenced S. gallolyticus UCN34 of the same biotype [52], [53], with 255 (11.4%) being either annotated as conserved hypothetical proteins or proteins with no database match. Out of the 1869 predicted CDS in the smaller ATCC 43144, 180 (9.6%) are hypothetical proteins without functional assignment.


Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.

Lin IH, Liu TT, Teng YT, Wu HL, Liu YM, Wu KM, Chang CH, Hsu MT - PLoS ONE (2011)

Circular representation of the S. gallolyticus ATCC 43143 and S. pasteurianus ATCC 43144 genomes.From the outside in, the outer two circles shows open reading frames oriented in the forward (red) and reverse (blue) direction, respectively. The third circle marks the rRNA gene operon (pink) and the fourth circle shows the tRNA genes (orange). The fifth circle shows GC skew, purple indicating negative values whereas olive for positive values. The inner-most circle shows the G+C% content plot.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102119&req=5

pone-0020519-g001: Circular representation of the S. gallolyticus ATCC 43143 and S. pasteurianus ATCC 43144 genomes.From the outside in, the outer two circles shows open reading frames oriented in the forward (red) and reverse (blue) direction, respectively. The third circle marks the rRNA gene operon (pink) and the fourth circle shows the tRNA genes (orange). The fifth circle shows GC skew, purple indicating negative values whereas olive for positive values. The inner-most circle shows the G+C% content plot.
Mentions: The genome of S. gallolyticus ATCC 43143 and S. pasteurianus ATCC 43144 each comprises a single circular chromosome of 2,362,241 bp and 2,100,077 bp respectively (Figure 1). The general features are presented in Table 1. The average G+C contents of both genomes are 37% and neither contains any plasmids. There are 61 tRNA genes and five rRNA operons in each chromosomes, with most of the tRNA genes situated close to rRNA operons. A total of 2246 protein-coding genes are predicted in ATCC 43143, much similar to the recently sequenced S. gallolyticus UCN34 of the same biotype [52], [53], with 255 (11.4%) being either annotated as conserved hypothetical proteins or proteins with no database match. Out of the 1869 predicted CDS in the smaller ATCC 43144, 180 (9.6%) are hypothetical proteins without functional assignment.

Bottom Line: We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans.This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced.The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.

View Article: PubMed Central - PubMed

Affiliation: Institute of BioMedical Informatics, National Yang-Ming University, Taipei, Taiwan.

ABSTRACT
Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection. Here, we present the complete genomes of S. gallolyticus ATCC 43143 (biotype I) and S. pasteurianus ATCC 43144 (biotype II.2). The genomic differences between the two biotypes were characterized with comparative genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length and encode 2246 and 1869 CDS respectively. The organization and genomic contents of both genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92%) and 1607 (86%) of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively. There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus genus has a small core-genome (constitute around 30% of total CDS) and substantial evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC 43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to contribute to the fitness and virulence of each of the two subspecies. We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans. This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.

Show MeSH
Related in: MedlinePlus