Open Access Research article

Evolutionary paths of streptococcal and staphylococcal superantigens

Kayo Okumura14, Yumi Shimomura1, Somay Yamagata Murayama25, Junji Yagi3, Kimiko Ubukata2, Teruo Kirikae1 and Tohru Miyoshi-Akiyama1*

Author Affiliations

1 Department of Infectious Diseases, National Center for Global Health and Medicine, 1-21-1, Shinjuku-ku, Tokyo, 162-8655, Japan

2 Graduate School of Infection Control Science, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo, 108–8641, Japan

3 Department of Microbiology and Immunology, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan

4 Department of Animal and Food Hygiene, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan

5 Present affiliation: College of Pharmacy, Nihon University, Narashinodai, Funabashi, Chiba, 274-8555, Japan

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BMC Genomics 2012, 13:404  doi:10.1186/1471-2164-13-404

Published: 17 August 2012

Additional files

Additional file 1:

Streptococcus isolates used in this study.

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Additional file 2:

Homology of S. dysgalactiae subsp. equisimilis GGS_124 with other bacteria at the genome level.

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Additional file 3:

List of oligonucleotide primers used in this study.

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Additional file 4:

Features of speG-negative strain specific regions.

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Additional file 5:

Summary of flaR and the dpp operon in each Streptococci strain.

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Additional file 6:

List of genes present in SSRI and SSR II.

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Additional file 7:

Phylogenetic tree of streptococcal and staphylococcal SAgs and SSL amino acid sequences. The phylogenetic tree was constructed using the Bayesian MCMC method, with 100,000 generations and a mixed amino acid evolution model. The resultant potential scale reduction factor was 1.078. Essentially the same result was obtained by changing the number of generations and using the amino acid evolution model (data not shown). The nucleotide sequences used for alignment are shown in Additional file 9. The resulting phylogenetic tree was composed of three clades, with clade I including only streptococcal SAgs, clade II including only staphylococcal SSLs, and clade III including SAgs from both species. Orthologous gene products, including SpeG and SMEZ in clade I, SSL-like proteins in clade II and SElW in clade III, are emphasized. Yersinia SAgs (YPMA, YPMB, and YPMC) were also included as an outgroup.

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Additional file 8:

Synteny mapping of the set-containing regions of Staphylococcus carnosus TM300 and S.aureus strains. Each position (bp) on each genome is shown in Additional file 10.

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Additional file 9:

List of Accession numbers for SAgs used in this study.

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Additional file 10:

List of Accession numbers for SAgs used in this study.

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