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Insights on virulence from the complete genome of Staphylococcus capitis.

Cameron DR, Jiang JH, Hassan KA, Elbourne LD, Tuck KL, Paulsen IT, Peleg AY - Front Microbiol (2015)

Bottom Line: Methylome analysis identified significant adenine methylation across the genome involving two distinct methylation motifs (1972 putative 6-methyladenine (m6A) residues identified).Putative adenine methyltransferases were also identified.Comparative analysis of AYP1020 and the closely related CoNS, S. epidermidis RP62a, revealed a host of virulence factors that likely contribute to S. capitis pathogenicity, most notably genes important for biofilm formation and a suite of phenol soluble modulins (PSMs); the expression/production of these factors were corroborated by functional assays.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Monash University Melbourne, VIC, Australia.

ABSTRACT
Staphylococcus capitis is an opportunistic pathogen of the coagulase negative staphylococci (CoNS). Functional genomic studies of S. capitis have thus far been limited by a lack of available complete genome sequences. Here, we determined the closed S. capitis genome and methylome using Single Molecule Real Time (SMRT) sequencing. The strain, AYP1020, harbors a single circular chromosome of 2.44 Mb encoding 2304 predicted proteins, which is the smallest of all complete staphylococcal genomes sequenced to date. AYP1020 harbors two large mobile genetic elements; a plasmid designated pAYP1020 (59.6 Kb) and a prophage, ΦAYP1020 (48.5 Kb). Methylome analysis identified significant adenine methylation across the genome involving two distinct methylation motifs (1972 putative 6-methyladenine (m6A) residues identified). Putative adenine methyltransferases were also identified. Comparative analysis of AYP1020 and the closely related CoNS, S. epidermidis RP62a, revealed a host of virulence factors that likely contribute to S. capitis pathogenicity, most notably genes important for biofilm formation and a suite of phenol soluble modulins (PSMs); the expression/production of these factors were corroborated by functional assays. The complete S. capitis genome will aid future studies on the evolution and pathogenesis of the coagulase negative staphylococci.

No MeSH data available.


Related in: MedlinePlus

Predicted phenol-soluble modulin (PSM) genes and amino acid sequences in S. capitis AYP1020. The genetic arrangement of phenol soluble modulin genes in AYP1020 (A) is highly similar when compared to S. epidermidis RP62a (B). In each case, PSMs are found on 4 distinct genetic loci. Predicted PSMs of S. capitis have high amino acid sequence identity when compared to S. epidermidis RP62a (C). AYP1020 has both α- and β-type PSMs, which are classed based on length. Each PSM contains an amphipathic α-helix, which is highlighted in yellow. AYP1020 has three distinct PSM β1 genes (a, c, and d), whereas RP62a has two identical copies of PSM β1 (a and b).
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Figure 5: Predicted phenol-soluble modulin (PSM) genes and amino acid sequences in S. capitis AYP1020. The genetic arrangement of phenol soluble modulin genes in AYP1020 (A) is highly similar when compared to S. epidermidis RP62a (B). In each case, PSMs are found on 4 distinct genetic loci. Predicted PSMs of S. capitis have high amino acid sequence identity when compared to S. epidermidis RP62a (C). AYP1020 has both α- and β-type PSMs, which are classed based on length. Each PSM contains an amphipathic α-helix, which is highlighted in yellow. AYP1020 has three distinct PSM β1 genes (a, c, and d), whereas RP62a has two identical copies of PSM β1 (a and b).

Mentions: PSMs are secreted amphipathic peptides that appear to have multiple functions in the pathogenicity of staphylococci (Wang et al., 2007b; Peschel and Otto, 2013). PSMs have been shown to be pro-inflammatory and possess cytolytic properties, contribute to biofilm development and have anti-microbial activity, as shown by selective Streptococcus pyogenes killing (Yao et al., 2005; Wang et al., 2007b; Cogen et al., 2010). The AYP1020 genome encodes for a number of peptides with high sequence similarity to the PSMs of S. epidermidis (Figures 5A,B). Like S. epidermidis, S. capitis AYP1020 encodes four α-type PSMs and four β-type PSMs (Figure 5C). The β-type PSMs are present in an operon, whereas the α-type PSMs are found in three distinct genomic locations. The hld gene, encoding the α-type PSM δ-toxin, is present within RNAIII, the key regulatory molecule of the accessory gene regulator system, Agr (Recsei et al., 1986). PSM peptides have an amphipathic α-helical structure, which causes longer retention times during liquid chromatography compared to most other proteins in culture supernatants (Joo and Otto, 2014).


Insights on virulence from the complete genome of Staphylococcus capitis.

Cameron DR, Jiang JH, Hassan KA, Elbourne LD, Tuck KL, Paulsen IT, Peleg AY - Front Microbiol (2015)

Predicted phenol-soluble modulin (PSM) genes and amino acid sequences in S. capitis AYP1020. The genetic arrangement of phenol soluble modulin genes in AYP1020 (A) is highly similar when compared to S. epidermidis RP62a (B). In each case, PSMs are found on 4 distinct genetic loci. Predicted PSMs of S. capitis have high amino acid sequence identity when compared to S. epidermidis RP62a (C). AYP1020 has both α- and β-type PSMs, which are classed based on length. Each PSM contains an amphipathic α-helix, which is highlighted in yellow. AYP1020 has three distinct PSM β1 genes (a, c, and d), whereas RP62a has two identical copies of PSM β1 (a and b).
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4585213&req=5

Figure 5: Predicted phenol-soluble modulin (PSM) genes and amino acid sequences in S. capitis AYP1020. The genetic arrangement of phenol soluble modulin genes in AYP1020 (A) is highly similar when compared to S. epidermidis RP62a (B). In each case, PSMs are found on 4 distinct genetic loci. Predicted PSMs of S. capitis have high amino acid sequence identity when compared to S. epidermidis RP62a (C). AYP1020 has both α- and β-type PSMs, which are classed based on length. Each PSM contains an amphipathic α-helix, which is highlighted in yellow. AYP1020 has three distinct PSM β1 genes (a, c, and d), whereas RP62a has two identical copies of PSM β1 (a and b).
Mentions: PSMs are secreted amphipathic peptides that appear to have multiple functions in the pathogenicity of staphylococci (Wang et al., 2007b; Peschel and Otto, 2013). PSMs have been shown to be pro-inflammatory and possess cytolytic properties, contribute to biofilm development and have anti-microbial activity, as shown by selective Streptococcus pyogenes killing (Yao et al., 2005; Wang et al., 2007b; Cogen et al., 2010). The AYP1020 genome encodes for a number of peptides with high sequence similarity to the PSMs of S. epidermidis (Figures 5A,B). Like S. epidermidis, S. capitis AYP1020 encodes four α-type PSMs and four β-type PSMs (Figure 5C). The β-type PSMs are present in an operon, whereas the α-type PSMs are found in three distinct genomic locations. The hld gene, encoding the α-type PSM δ-toxin, is present within RNAIII, the key regulatory molecule of the accessory gene regulator system, Agr (Recsei et al., 1986). PSM peptides have an amphipathic α-helical structure, which causes longer retention times during liquid chromatography compared to most other proteins in culture supernatants (Joo and Otto, 2014).

Bottom Line: Methylome analysis identified significant adenine methylation across the genome involving two distinct methylation motifs (1972 putative 6-methyladenine (m6A) residues identified).Putative adenine methyltransferases were also identified.Comparative analysis of AYP1020 and the closely related CoNS, S. epidermidis RP62a, revealed a host of virulence factors that likely contribute to S. capitis pathogenicity, most notably genes important for biofilm formation and a suite of phenol soluble modulins (PSMs); the expression/production of these factors were corroborated by functional assays.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Monash University Melbourne, VIC, Australia.

ABSTRACT
Staphylococcus capitis is an opportunistic pathogen of the coagulase negative staphylococci (CoNS). Functional genomic studies of S. capitis have thus far been limited by a lack of available complete genome sequences. Here, we determined the closed S. capitis genome and methylome using Single Molecule Real Time (SMRT) sequencing. The strain, AYP1020, harbors a single circular chromosome of 2.44 Mb encoding 2304 predicted proteins, which is the smallest of all complete staphylococcal genomes sequenced to date. AYP1020 harbors two large mobile genetic elements; a plasmid designated pAYP1020 (59.6 Kb) and a prophage, ΦAYP1020 (48.5 Kb). Methylome analysis identified significant adenine methylation across the genome involving two distinct methylation motifs (1972 putative 6-methyladenine (m6A) residues identified). Putative adenine methyltransferases were also identified. Comparative analysis of AYP1020 and the closely related CoNS, S. epidermidis RP62a, revealed a host of virulence factors that likely contribute to S. capitis pathogenicity, most notably genes important for biofilm formation and a suite of phenol soluble modulins (PSMs); the expression/production of these factors were corroborated by functional assays. The complete S. capitis genome will aid future studies on the evolution and pathogenesis of the coagulase negative staphylococci.

No MeSH data available.


Related in: MedlinePlus