We propose Streptococcus mutans UA159 contains a genomic island resulting from horizontal gene transfer. This 7.4 kb genomic island encompasses genes with low G+C content compared to the genome average of 37%. It is constituted of a sorbose PTS system, two genes related to sugar metabolism, a sucrose operon transcriptional repressor, and a transposase fragment (Fig. 1). The island boundaries were supported by its location between a tRNA-Leu and a tRNA-Thr: Deviant G+C content, presence of mobility elements, and flanking by tRNA's are characteristics which are commonly observed with horizontal transfer events (see GENOMIC ISLANDS).

FIGURE 1: Genomic Island Indicated in Blue

LANL GeneId	Definition	Gene Name	GC%	Gene Length (bp)
SMu0085	transposase fragment	tpn	39	168
SMu0086	DNA-directed RNA polymerase, delta subunit	rpoE	37	486
SMu0087	CTP synthetase	pyrG	39	1608
SMu0088	fructose-1,6-biphosphate aldolase	sorG, fbaA	41	879
SMu0089	sorbose PTS system, IIB component	sorD	32	489
SMu0090	sorbose PTS system, IIC component	sorC	34	795
SMu0091	sorbose PTS system, IID component	sorB	35	819
SMu0092	sorbose PTS system, IIA component	sorA	34	414
SMu0093	glycosyl hydrolase, alpha-glucosidase	yicI	35	2193
SMu0094	SCR operon transcriptional repressor	scrR	34	996
SMu0095	transposase fragment	tpn	46	234
SMu0096	hypothetical protein		21	168
SMu0097	hypothetical protein		29	135
SMu0098	conserved hypothetical protein		33	1098
SMu0099	transcriptional regulator		30	858
SMu0100	transcriptional regulator, Rpir family		35	747
SMu0101	fructose-1-phosphate-kinase	pfk	37	930

* Yebra, et al have identified eight ORFs in Lactobacillus casei ATCC393 whose products are involved in L-sorb ose transport and metabolism [7]. This is the source of the "sor" gene names provided.

Gene SMu0088, fructose-1,6-biphosphate aldolase, may or may not be part of this island. On the one hand, is it observed with the sorbose PTS system in other species. On the other hand, it has a high G+C content which is not consistent with the other genes in the island. Also, it does not have any paralogs in the genome (i.e., if this gene was in fact laterally transferred, there is not a duplicate copy). The PTS transporters consist of three subunits, IIA, IIB, and IIC. The exception is the mannose family transporters, which also contains the subunit, IID.

The mannose class PTS transporter:
1) is the primary PTS for glucose transport in bacteria such as Lactobacilli or Streptococci
2) contains an additional IID domain
3) has a relatively wide variety of substrates including glucose, mannose, sorbose, galactosamine, and fructose.

The mannose class PTS transporters have a limited distribution; most are found in species belonging to Firmicutes and gamma-Proteobacteria, with the exception of the transporter found in Fusobacterium nucleatum. Most bacteria with mannose class PTS transporters may thrive in mucosal surfaces of animals, either as pathogens or saprophytes [8]. In addition, some of these transporters are found with genes encoding proteins related to polysaccharide degradation. Thus, PTS transporters may assist bacteria in adapting to these habitats [8].

The nearest neighbor for the S mutans sor operon is Lactobacillus casei ATCC334. This is curious because the GC content of L.casei, 47%, is not similar to that of S.mutans, 37%. However, the next best neighbor, Lactobacillus johnsonii NCC533 has a similar GC content to S.mutans at 35%. Both of these blast hits are highly orthologous (35-60% similarities). It is interesting to note that the top blast hits are not to other Streptococci.

The cluster of genes found in this potential island are maintained in a number of Streptococci and Lactobacilli, indicating it provides an important functionality (Fig. 2).

FIGURE 2: Sor Operon Gene Order

Streptococcus mutans UA159		         G - B - C - D - A - L - S - T

Lactobacillus casei ATCC334		             B - C - D - L - A  

Lactobacillus casei ATCC393	     E - R - F - A - B - C - D - G	

Lactobacillus johnsonii NCC 533	                     B - C - D - A - O - H/S*

Streptococcus pneumoniae R6		             B - C - D - A

Streptococcus pneumoniae TIGR4		             B - C - D - A

Fusobacterium nucleatum ATCC25586	             D - C - B - A


* This hypothetical protein has blast hits to SCR operon transcriptional repressor.

GLOSSARY:

Symbol	Definition	Gene Name
A	PTS system, EIIA	sorA
B	PTS system, EIIB	sorB
C	PTS system, EIIC	sorC
D	PTS system, EIID	sorD
E	L-Sorbose-1 P reductase	sorE
F	D-Sorbitol-6 P dehydrogenase	sorF
G	D-Fructose-1,6 bP aldolase	sorG, fbaA
R	Transcriptional regulator	sorR
L	glycosyl hydrolase, alpha-glucosidase	yicI
S	SCR operon transcriptional repressor	scrR
T	transposase fragment	tpn
O	oligo-1,6-glucosidase
H	hypothetical protein

References:

1.  Ajdic D, McShan WM, McLaughlin RE, et al.
Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen.
Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14434-9. Epub 2002 Oct 23. 
PMID: 12397186 [PubMed - indexed for MEDLINE]

2.  Boyd DA, Thevenot T, Gumbmann M, Honeyman AL, Hamilton IR.
Identification of the operon for the sorbitol (Glucitol) Phosphoenolpyruvate:Sugar
phosphotransferase system in Streptococcus mutans.
Infect Immun. 2000 Feb;68(2):925-30. 
PMID: 10639465 [PubMed - indexed for MEDLINE]

3.  Duncan MJ.
Genomics of oral bacteria.
Crit Rev Oral Biol Med. 2003;14(3):175-87. Review. 
PMID: 12799321 [PubMed - indexed for MEDLINE]

4.  Saier MH Jr, Reizer J.
Proposed uniform nomenclature for the proteins and protein domains of the bacterial phosphoenolpyruvate: sugar phosphotransferase system.
J Bacteriol. 1992 Mar;174(5):1433-8. No abstract available. 
PMID: 1537788 [PubMed - indexed for MEDLINE]

5.  Tettelin H, Nelson KE, Paulsen IT, et al.
Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.
Science. 2001 Jul 20;293(5529):498-506. 
PMID: 11463916 [PubMed - indexed for MEDLINE]

6.  Wilkins JC, Homer KA, Beighton D.
Analysis of Streptococcus mutans proteins modulated by culture under acidic conditions.
Appl Environ Microbiol. 2002 May;68(5):2382-90. 
PMID: 11976112 [PubMed - indexed for MEDLINE]

7.  Yebra MJ, Veyrat A, Santos MA, Perez-Martinez G.
Genetics of L-sorbose transport and metabolism in Lactobacillus casei.
J Bacteriol. 2000 Jan;182(1):155-63. 
PMID: 10613875 [PubMed - indexed for MEDLINE]

8.  Zuniga M, Comas I, Linaje R, et al.
Horizontal Gene Transfer in the Molecular Evolution of Mannose PTS Transporters.
Mol Biol Evol. 2005 Aug;22(8):1673-1685. 
PMID: 16006479 [PubMed - as supplied by publisher]