Streptococcus mutans strain UA159 Genome Sequencing
The sequence of the 2,030,936 bp Streptococcus mutans strain UA159 Genome is completed
and the results published in the October 29, 2002 issue of Proceedings National Academy of Sciences USA.
Dragana Ajdic, William M. McShan, Robert E. McLaughlin, Gorana Savic,
Jin Chang, Matthew B. Carson, Charles Primeaux, Runying Tian,
Steve Kenton, Honggui Jia, Shaoping Lin, Yudong Qian, Shuling Li,
Hua Zhu, Fares Najar, Hongshing Lai, Jim White, Bruce A. Roe, and Joseph J.
Genome sequence of Streptococcus mutans UA159,
a cariogenic dental pathogen.
PNAS 99, 14434-14439 (2002).
The annotated genomic sequence can be accessed through GenBank (assession no. AEO14133).
Streptococcus mutans strain UA159 Genome Sequencing Progress
We have produced and have sequenced both ends of the pUC sub-clones from shotgun libraries from genomic DNA isolated from Streptococcus mutans
serotype C, strain UA159 (ATCC700610)
obtained from Page Caufield at University Alabama Birmingham.
This NIH funded project is a joint collaboration
between our Genome Center at the University of Oklahoma in Norman, OK and
Dr. Joe Ferretti's laboratory at in the Department of Microbiology and
Immunology at the University of Oklahoma Health Sciences Center in Oklahoma
Our strategy was to sequence approximately 12,000 individual, shotgun-based, double stranded templates generated from a randomly sheared library of the Streptococcus mutans genome, with both the universal forward and reverse pUC sequencing primers.
When this shotgun phase was completed we moved to a directed
custom synthetic primer-based approach for closure and quality
improvement to complete the sequence of the genome to a high
level of accuracy.
All of our data in contigs greater that 1kb is
publically available in accord with the Bermuda Agreement on this web site.
As of 10-29-98 we switched to Phred980904.a and Phrap980831
and also increased our database assembly stringency from the default
values of PHRAP's min_match and min_score by doubling them to produce
high stringency assembled data that is more accurate.
As of 04-12-01 the Streptococcus mutans strain UA159 Genome
shotgun and closure phase have been completed and the genomic sequence
has been assembled into one, circular contig.
View the latest high stringency Streptococcus mutans Statistics
Search the Streptococcus mutans Genome sequence data
Obtaining the sequence data via ftp
All of our shotgun sequence data is available via ftp (see below) but at the present time, the various contigs are in "random" order and do not correspond to any specific relationship one to another.
Please be aware that the order and contig number will change with each new
release of data.
Caution: the data has been neither proof read nor edited and thus should be
considered preliminary raw sequence data.
Also, because the sequence assembly program, Phrap,
has the tendency to include inaccurate sequence reads on the ends of contigs, be
cautious when using sequences within 1-200 bases of the ends of individual contigs.
Please take this into account when using this data
Obtaining the Streptococcus mutans Sequencing Data via ftp
If instead, you would rather ftp this file directly, you can ftp to
ftp.genome.ou.edu (logon as anonymous with password your e-mail address).
Read the 00readme file in the ftp directory to determine which files you are interested in.
The Streptococcus mutans strain being sequenced can be
obtained from the ATCC as ATCC700610.
At the present time, none of the shotgun clones are available, but we
anticipate at some point to generate a set of ordered sub-clones that will be made available throught the ATCC.
Literature Reference Describing Strain being sequenced
Murchison HH et al. Transformation of Streptococcus mutans with
chromosomal and shuttle plasmid (pYA629) DNAs. Infect. Immun. 54:
Wexler DL et al. Characteristics and cariogenicity of a
fructanase-defective Streptococcus mutants strain. Infect. Immun. 60:
Tao L et al. Transformation efficiency of EMS-induced mutants of
Streptococcus mutans of altered cell shape. J. Dent. Res. 72:
Quivey RG Jr et al. Acid adaptation in Streptococcus mutans UA159
alleviates sensitization to environmental stress due to RecA
Microbiol. Lett. 126: 257-261, 1995
Burne RA et al. Cariogenicity of Streptococcus mutans strains with
defects in fructan metabolism assessed in a program-fed
specific-pathogen-free rat model. J. Dent. Res. 75: 1572-1577, 1996
Should you find this data useful and wish to reference it, please acknowledge
the Streptococcal mutans Genome Sequencing Project funded by USPHS/NIH grant from the Dental Institute
and B. A. Roe, R. Y. Tian, H. G. Jia, Y. D. Qian, S. P. Lin, S. Li, S. Kenton, H. Lai, J. D. White, R. E. McLaughlin, M. McShan, D. Ajdic and J. Ferretti.
If possible, please send us both the literature citation once published,
and a copy of the manuscript.
Thanks, Bruce Roe, RunYing Tian, HongGui Jia, YuDong Qian, Shaoping Lin, Suling Li, Steve Kenton, HongShing Lai, Jim D. White, Bob McLaughlin, Mike McShan, Dragana Ajdic and Joseph Ferretti.
The University of Oklahoma, Department of Chemistry and Biochemistry, Norman,
and The University of Oklahoma Health Sciences Center, Department of Microbiology
and Immunology, Oklahoma City, Oklahoma 73190
Joe Ferretti, Joseph-Ferretti@uokhsc.edu
Bob McLaughlin, firstname.lastname@example.org
Dragana Ajdic, email@example.com
Mike McShan, wmcshan@REX.RE.uokhsc.edu
Bruce Roe, firstname.lastname@example.org
Bruce Roe, email@example.com