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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, ╬ŽAYP1020 (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

Circular representation of the S. capitis AYP1020 chromosome and its plasmid, pAYP1020. For the chromosome, the first (innermost) ring indicates the GC skew, followed by the GC content (second ring). The third ring indicates the degree of amino acid identity across all CDS of S. capitis AYP1020 compared to S. epidermidis RP62a, as determined by BLASTp and scaled according to percent identity as indicated in the key (Altschul et al., 1997). Colored arrows on the fourth and seventh rings represent the following COG categories (Tatusov et al., 2000); A, B, J, K, L, information and storage and processing; D, O, M, N, P, T, U, V, W, Y, Z, cellular processes and signaling; C, G, E, F, H, I, Q, metabolism; R and S, poorly characterized, on the reverse and forward strands, respectively. The fifth and sixth rings represent the CDS (blue), tRNA (maroon), and rRNA (purple) on the reverse and forward strands, respectively. For the genome, the scale displayed in the center of the graphic represents 500 kb. For the plasmid, the scale represents 5 kb. The images were generated using CGview (Grant et al., 2012).
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Figure 2: Circular representation of the S. capitis AYP1020 chromosome and its plasmid, pAYP1020. For the chromosome, the first (innermost) ring indicates the GC skew, followed by the GC content (second ring). The third ring indicates the degree of amino acid identity across all CDS of S. capitis AYP1020 compared to S. epidermidis RP62a, as determined by BLASTp and scaled according to percent identity as indicated in the key (Altschul et al., 1997). Colored arrows on the fourth and seventh rings represent the following COG categories (Tatusov et al., 2000); A, B, J, K, L, information and storage and processing; D, O, M, N, P, T, U, V, W, Y, Z, cellular processes and signaling; C, G, E, F, H, I, Q, metabolism; R and S, poorly characterized, on the reverse and forward strands, respectively. The fifth and sixth rings represent the CDS (blue), tRNA (maroon), and rRNA (purple) on the reverse and forward strands, respectively. For the genome, the scale displayed in the center of the graphic represents 500 kb. For the plasmid, the scale represents 5 kb. The images were generated using CGview (Grant et al., 2012).

Mentions: Phylogenetic analysis revealed a close relationship between AYP1020 and other S. capitis strains for which genome sequence information was available, particularly S. capitis SK14 and S. capitis VCU116 (Figure 1). The analysis also shows that S. capitis has closer evolutionary links to S. epidermidis than other clinically relevant coagulase negative staphylococci (Figure 1). S. capitis strain AYP1020 has a 2,443,605 bp chromosome with a GC content of 33.0% (Figure 2). The chromosome is predicted to contain 2304 protein-coding DNA sequences, six rRNA operons, 63 tRNA genes and a single tmRNA (Table 1). S. capitis AYP1020 represents the smallest genome of all closed staphylococcal genomes sequenced to date, with the fewest predicted CDS.


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)

Circular representation of the S. capitis AYP1020 chromosome and its plasmid, pAYP1020. For the chromosome, the first (innermost) ring indicates the GC skew, followed by the GC content (second ring). The third ring indicates the degree of amino acid identity across all CDS of S. capitis AYP1020 compared to S. epidermidis RP62a, as determined by BLASTp and scaled according to percent identity as indicated in the key (Altschul et al., 1997). Colored arrows on the fourth and seventh rings represent the following COG categories (Tatusov et al., 2000); A, B, J, K, L, information and storage and processing; D, O, M, N, P, T, U, V, W, Y, Z, cellular processes and signaling; C, G, E, F, H, I, Q, metabolism; R and S, poorly characterized, on the reverse and forward strands, respectively. The fifth and sixth rings represent the CDS (blue), tRNA (maroon), and rRNA (purple) on the reverse and forward strands, respectively. For the genome, the scale displayed in the center of the graphic represents 500 kb. For the plasmid, the scale represents 5 kb. The images were generated using CGview (Grant et al., 2012).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Circular representation of the S. capitis AYP1020 chromosome and its plasmid, pAYP1020. For the chromosome, the first (innermost) ring indicates the GC skew, followed by the GC content (second ring). The third ring indicates the degree of amino acid identity across all CDS of S. capitis AYP1020 compared to S. epidermidis RP62a, as determined by BLASTp and scaled according to percent identity as indicated in the key (Altschul et al., 1997). Colored arrows on the fourth and seventh rings represent the following COG categories (Tatusov et al., 2000); A, B, J, K, L, information and storage and processing; D, O, M, N, P, T, U, V, W, Y, Z, cellular processes and signaling; C, G, E, F, H, I, Q, metabolism; R and S, poorly characterized, on the reverse and forward strands, respectively. The fifth and sixth rings represent the CDS (blue), tRNA (maroon), and rRNA (purple) on the reverse and forward strands, respectively. For the genome, the scale displayed in the center of the graphic represents 500 kb. For the plasmid, the scale represents 5 kb. The images were generated using CGview (Grant et al., 2012).
Mentions: Phylogenetic analysis revealed a close relationship between AYP1020 and other S. capitis strains for which genome sequence information was available, particularly S. capitis SK14 and S. capitis VCU116 (Figure 1). The analysis also shows that S. capitis has closer evolutionary links to S. epidermidis than other clinically relevant coagulase negative staphylococci (Figure 1). S. capitis strain AYP1020 has a 2,443,605 bp chromosome with a GC content of 33.0% (Figure 2). The chromosome is predicted to contain 2304 protein-coding DNA sequences, six rRNA operons, 63 tRNA genes and a single tmRNA (Table 1). S. capitis AYP1020 represents the smallest genome of all closed staphylococcal genomes sequenced to date, with the fewest predicted CDS.

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, ╬ŽAYP1020 (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