Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen

Abstract

Streptococcus mutans is the leading cause of dental caries (tooth decay) worldwide and is considered to be the most cariogenic of all of the oral streptococci. The genome of S. mutans UA159, a serotype c strain, has been completely sequenced and is composed of 2,030,936 base pairs. It contains 1,963 ORFs, 63% of which have been assigned putative functions. The genome analysis provides further insight into how S. mutans has adapted to surviving the oral environment through resource acquisition, defense against host factors, and use of gene products that maintain its niche against microbial competitors. S. mutans metabolizes a wide variety of carbohydrates via nonoxidative pathways, and all of these pathways have been identified, along with the associated transport systems whose genes account for almost 15% of the genome. Virulence genes associated with extracellular adherent glucan production, adhesins, acid tolerance, proteases, and putative hemolysins have been identified. Strain UA159 is naturally competent and contains all of the genes essential for competence and quorum sensing. Mobile genetic elements in the form of IS elements and transposons are prominent in the genome and include a previously uncharacterized conjugative transposon and a composite transposon containing genes for the synthesis of antibiotics of the gramicidin/bacitracin family; however, no bacteriophage genomes are present.

Fig 1.

Circular representation of the S. mutans, strain UA159 genome. The outer two circles show the position of the probable ORFs on the complementary DNA strands. The ORFs have been color coded by functional category (the color legend is presented in Fig. 3, which is published as supporting information on the PNAS web site). The remaining circles are, proceeding inward: the location of the mobile genetic elements, the ABC transporters involved in the sugar metabolism, the PTS transporters and PTS Enzyme I, the position of the ribosomal (black) and tRNA (green), the %G+C of the sequence, and the %G+C deviation by strand.

Fig 2.

Reconstruction of specific metabolic pathways and transport mechanisms in S. mutans. Based on the annotated genome sequence, extracellular and intracellular sugar metabolism and metabolism of organic compounds are shown. Transporters are grouped by substrate specificity: red, carbohydrates; green, amino acids/peptides; gold, inorganic cations; blue, inorganic anions; purple, DNA/nucleotides; black, drugs and unclassified. Question marks indicate uncertainty of substrate specificity. Arrows represent the direction of solute transport. Each figure shape represents the specific type of transporter: …… gtfB, glucosyltransferase-I; gtfC, glucosyltransferase-SI; gtfD, glucosyltransferase-S; dexA, dextranase; dexB, dextran glucosidase; ftf, fructosyltransferase; fruA, fructanase; ATP, adenosine monophosphate; ADP, adenosine diphosphate; P, phosphate.