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J Bacteriol. 2009 December; 191(23): 7378–7379.
Published online 2009 October 9. doi:  10.1128/JB.01203-09
PMCID: PMC2786557

Genome Sequence of Aggregatibacter actinomycetemcomitans Serotype c Strain D11S-1 [down-pointing small open triangle]

Abstract

Aggregatibacter actinomycetemcomitans is a major etiological agent of periodontitis. Here we report the complete genome sequence of serotype c strain D11S-1, which was recovered from the subgingival plaque of a patient diagnosed with generalized aggressive periodontitis.

Aggregatibacter actinomycetemcomitans is a major etiologic agent of human periodontal disease, in particular aggressive periodontitis (12). The natural population of A. actinomycetemcomitans is clonal (7). Six A. actinomycetemcomitans serotypes are distinguished based on the structural and serological characteristics of the O antigen of LPS (6, 7). Three of the serotypes (a, b, and c) comprise >80% of all strains, and each serotype represents a distinct clonal lineage (1, 6, 7). Serotype c strain D11S-1 was cultured from a subgingival plaque sample of a patient diagnosed with generalized aggressive periodontitis. The complete genome sequencing of the strain was determined by 454 pyrosequencing (10), which achieved 25× coverage. Assembly was performed using the Newbler assembler (454, Branford, CT) and generated 199 large contigs, with 99.3% of the bases having a quality score of 40 and above. The contigs were aligned with the genome of the sequenced serotype b strain HK1651 (http://www.genome.ou.edu/act.html) using software written in house. The putative contig gaps were then closed by primer walking and sequencing of PCR products over the gaps. The final genome assembly was further confirmed by comparison of an in silico NcoI restriction map to the experimental map generated by optical mapping (8). The genome structure of the D11S-1 strain was compared to that of the sequenced strain HK1651 using the program MAUVE (2, 3). The automated annotation was done using a protocol similar to the annotation engine service at The Institute for Genomic Research/J. Craig Venter Institute with some local modifications. Briefly, protein-coding genes were identified using Glimmer3 (4). Each protein sequence was then annotated by comparing to the GenBank nonredundant protein database. BLAST-Extend-Repraze was applied to the predicted genes to identify genes that might have been truncated due to a frameshift mutation or premature stop codon. tRNA and rRNA genes were identified by using tRNAScan-SE (9) and a similarity search to our in-house RNA database, respectively.

The D11S-1 circular genome contains 2,105,764 nucleotides, a GC content of 44.55%, 2,134 predicted coding sequences, and 54 tRNA and 19 rRNA genes (see additional data at http://expression.washington.edu/bumgarnerlab/publications.php). The distribution of predicted genes based on functional categories was similar between D11S-1 and HK1651 (http://expression.washington.edu/bumgarnerlab/publications.php). One hundred six and 86 coding sequences were unique to strain D11S-1 and HK1651, respectively (http://expression.washington.edu/bumgarnerlab/publications.php). Genomic islands were identified based on annotations for strain HK1651 and based on manual inspection of contiguous D11S-1 specific DNA regions with G+C bias (http://expression.washington.edu/bumgarnerlab/publications.php). Among 12 identified genomics islands, 5 (B, C, D, E and G; cytolethal distending toxin gene cluster, tight adherence gene cluster, O-antigen biosynthesis and transport gene cluster, leukotoxin gene cluster, and lipoligosaccharide biosynthesis enzyme gene, respectively) correspond to islands 2 to 5 and 8 of strain HK1651 (http://www.oralgen.lanl.gov/) (5). Island F (~5 kb) is homologous to a portion of the 12.5-kb island 7 in HK1651. Five genomic islands (H to L) were unique to strain D11S-1. The remaining island (A) is a fusion of genomic islands 1 and 6, in strain HK1651. The genome of D11S-1 is largely in synteny with the genome of the sequenced serotype b strain HK1651 but contained several large-scale genomic rearrangements.

Strain D11S-1 harbors a 43-kb bacteriophage and two plasmids of 31 and 23 kb (http://expression.washington.edu/bumgarnerlab/publications.php). Excluding an ~9-kb region of low homology, the phage showed >90% nucleotide sequence identity with AaΦ23 (11). A 49-bp attB site (11) was identified at coordinates 2,024,825 to 2,024,873. The location of the inserted phage was identified in the optical map of strain D11S-1 and further confirmed by PCR amplification and sequencing of the regions flanking the insertion site. A closed circular form of the phage was also detected in strain D11S-1 by PCR analysis of the phage ends. The 23-kb plasmid is homologous to pVT745 (92% nucleotide identities). The 31-kb plasmid is a novel plasmid. It has significant homologies in short regions (<2 kb) to Haemophilus influenzae biotype aegyptius plasmid pF1947 and other plasmids.

Nucleotide sequence accession numbers.

The complete genome sequences of A. actinomycetemcomitans strain D11S-1 and its phage and plasmids have been assigned GenBank accession numbers CP001733, GQ866233, GQ866234, and GQ866235, respectively.

Acknowledgments

This study was supported by NIDCR grant R01 DE12212.

We are grateful to Bruce Roe, Fares Najar, Sandy Clifton, Tom Ducey, Lisa Lewis, and Dave Dyer for the use of unpublished nucleotide sequence data from the A. actinomycetemcomitans Genome Sequencing Project at The University of Oklahoma.

Footnotes

[down-pointing small open triangle]Published ahead of print on 9 October 2009.

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