Complete genome sequence of the ureolytic Streptococcus salivarius strain 57.I.
ABSTRACT Streptococcus salivarius 57.I is one of the most abundant and highly ureolytic bacteria in the human mouth. It can utilize urea as the sole nitrogen source via the activity of urease. Complete genome sequencing of S. salivarius 57.I revealed a chromosome and a phage which are absent in strain SK126.
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ABSTRACT: Ureases are multisubunit enzymes requiring Ni(2+) for activity. The low pH-inducible urease gene cluster in Streptococcus salivarius 57.I is organized as an operon, beginning with ureI, followed by ureABC (structural genes), and ureEFGD (accessory genes). Urease biogenesis also requires a high-affinity Ni(2+) uptake system. By searching the partial genome sequence of a closely related organism, Streptococcus thermophilus LMG18311, three open reading frame (ORFs) homologous to those encoding proteins involved in cobalamin biosynthesis and cobalt transport (cbiMQO) were identified immediately 3' to the ure operon. To determine whether these genes were involved in urease biogenesis by catalyzing Ni(2+) uptake in S. salivarius, regions 3' to ureD were amplified by PCRs from S. salivarius by using primers identical to the S. thermophilus sequences. Sequence analysis of the products revealed three ORFs. Reverse transcriptase PCR was used to demonstrate that the ORFs are transcribed as part of the ure operon. Insertional inactivation of ORF1 with a polar kanamycin marker completely abolished urease activity and the ability to accumulate (63)Ni(2+) during growth. Supplementation of the growth medium with NiCl(2) at concentrations as low as 2.5 micro M partially restored urease activity in the mutant. Both wild-type and mutant strains showed enhanced urease activity when exogenous Ni(2+) was provided at neutral pH. Enhancement of urease activity by adding nickel was regulated at the posttranslational level. Thus, ORF1, ORF2, and ORF3 are part of the ure operon, and these genes, designated ureM, ureQ, and ureO, respectively, likely encode a Ni(2+)-specific ATP-binding cassette transporter.Journal of Bacteriology 01/2004; 185(23):6773-9. · 3.19 Impact Factor
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ABSTRACT: The hydrolysis of urea by urease enzyme of oral bacteria is believed to have a major impact on oral microbial ecology and to be intimately involved in oral health and diseases. To begin to understand the biochemistry and genetics of oral ureolysis, a study of the urease of Streptococcus salivarius, a highly ureolytic organism which is present in large numbers on the soft tissues of the oral cavity, has been initiated. By using as a probe a 0.6-kpb internal fragment of the S. salivarius 57.I ureC gene, two clones from subgenomic libraries of S. salivarius 57.I in an Escherichia coli plasmid vector were identified. Nucleotide sequence analysis revealed the presence of one partial and six complete open reading frames which were most homologous to ureIAB-CEFGD of other ureolytic bacteria. Plasmid clones were generated to construct a complete gene cluster and used to transform E. coli and Streptococcus gordonii DL1, a nonureolytic, dental plaque microorganism. The recombinant organisms expressed high levels of urease activity when the growth medium was supplemented with NiCl2. The urease enzyme was purified from E. coli, and its biochemical properties were compared with those of the urease produced by S. salivarius and those of the urease produced by S. gordonii carrying the plasmid-borne ure genes. In all cases, the enzyme had a Km of 3.5 to 4.1 mM, a pH optimum near 7.0, and a temperature optimum near 60 degrees C. S. gordonii carrying the urease genes was then demonstrated to have a significant capacity to temper glycolytic acidification in vitro in the presence of concentrations of urea commonly found in the oral cavity. The ability to genetically engineer plaque bacteria that can modulate environmental pH through ureolysis will open the way to using recombinant ureolytic organisms to test hypotheses regarding the role of oral ureolysis in dental caries, calculus formation, and periodontal diseases. Such recombinant organisms may eventually prove useful for controlling dental caries by replacement therapy.Infection and Immunity 03/1996; 64(2):585-92. · 4.07 Impact Factor
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ABSTRACT: A CadDX system that confers resistance to Cd(2+) and Zn(2+) was identified in Streptococcus salivarius 57.I. Unlike with other CadDX systems, the expression of the cad promoter was negatively regulated by CadX, and the repression was inducible by Cd(2+) and Zn(2+), similar to what was found for CadCA systems. The lower G+C content of the S. salivarius cadDX genes suggests acquisition by horizontal gene transfer.Applied and environmental microbiology 04/2008; 74(5):1642-5. · 3.69 Impact Factor
JOURNAL OF BACTERIOLOGY, Oct. 2011, p. 5596–5597
Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Vol. 193, No. 19
Complete Genome Sequence of the Ureolytic
Streptococcus salivarius Strain 57.I
Jianing Geng,1Szu-Chuan Huang,2Shuangli Li,1Songnian Hu,1and Yi-Ywan M. Chen2,3*
The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences,
100029 Beijing, People’s Republic of China,1and Department of Microbiology and Immunology2and Research Center for
Pathogenic Bacteria,3College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
Received 27 June 2011/Accepted 18 July 2011
Streptococcus salivarius 57.I is one of the most abundant and highly ureolytic bacteria in the human mouth.
It can utilize urea as the sole nitrogen source via the activity of urease. Complete genome sequencing of S.
salivarius 57.I revealed a chromosome and a phage which are absent in strain SK126.
Streptococcus salivarius, a member of the salivarius group of
the viridans group streptococci, is one of the early colonizers of
the epithelium and a common isolate of the human oral cavity
(10). When S. salivarius gains entrance to the bloodstream, it
may cause severe systemic infections (13). Although not all S.
salivarius strains synthesize urease, the ureolytic activity of S.
salivarius strain 57.I is the major alkali generation machinery in
the oral cavity that plays an essential role in maintaining oral
pH homeostasis and balancing dental plaque ecology (5, 17).
Here we report the complete genome and annotation of the
ureolytic strain 57.I and compared the genome with that of
The complete genome sequence of S. salivarius strain 57.I
was determined via a whole-genome shotgun approach em-
ploying Roche 454 pyrosequencing on a GS-FLX at 454 Life
Sciences. A total of 272,194 high-quality reads were assembled
by using Roche’s Newbler assembler with approximately 50?
sequence coverage of the entire genome. The order of the
contigs was arranged initially based on the gene order of S.
salivarius strain SK126 chromosome (ACLO00000000), and
the gaps between contigs were then finished by the multiplex
PCR and primer walking method. The resulting sequence was
edited by the phred/phrap/consed software package (8, 9, 11,
12). The protein-coding genes, tRNAs, and rRNA were pre-
dicted by Glimmer 3.0, tRNA-SE, and RNAmmer (7, 14, 15),
respectively. The functions of all genes were predicted by
searching against the NCBI nonredundant protein database,
cluster of orthologous groups (COGs), and InterProScan, and
the metabolic pathways were reconstructed by using the Kyoto
Encyclopedia of Genes and Genomes (KEGG) (1, 16, 18).
The genome has one circular DNA molecule with a GC
content of 39.93% and one phage DNA with a 41.24% GC
content. The chromosome DNA is 2,138,805 bp in length,
carrying 1,942 predicted open reading frames (ORFs), 68 pre-
dicted tRNA genes encoding all 20 amino acids, and 6 rRNA
operons containing 5S, 16S, and 23S RNA genes. Additionally,
there are two clusters of regularly interspaced short palin-
dromic repeats (CRISPRs) and two potential CRISPRs in the
chromosome. The phage DNA is 40,758 bp in length and
encodes 55 proteins. Comparative genomic analysis of S. sali-
varius strains 57.I and SK126 revealed 164 ORFs that are
unique in S. salivarius strain 57.I. These genes include the ure
operon of 11 genes, encoding all proteins required for assem-
bly of a functional urease (2, 3, 6), the cadDX operon, encoding
a system for cadmium and zinc resistance (4), and a cluster of
genes encoding sugar transferases involved in extracellular
polysaccharide synthesis (Ssal_01171-01174 and Ssal_01176-
01177), indicating that these two strains are fundamentally
different. The complete genome of strain 57.I will allow for
comparative genomics to further characterize the polymor-
phisms of S. salivarius strains and all species within the sali-
Nucleotide sequence accession numbers. The complete
genome information of S. salivarius strain 57.I was deposited
in GenBank under the accession numbers CP002888 and
This work was supported in part by the Chang Gung Memorial
Hospital (CMRPD10011) and the intramural funding of the Research
Center for Pathogenic Bacteria of Chang Gung University.
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* Corresponding author. Mailing address: Department of Microbi-
ology and Immunology, College of Medicine, Chang Gung University,
259 Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan, Taiwan 333. Phone:
886-3-2118800, ext. 3352. Fax: 886-3-2118700. E-mail: mchen@mail
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