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Journal of Bacteriology, July 2009, p. 4693-4694, Vol. 191, No. 14
0021-9193/09/$08.00+0     doi:10.1128/JB.00447-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

GENOME ANNOUNCEMENT

Complete Genome Sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700{triangledown}

Maria Pia Di Bonaventura,1 Rob DeSalle,1* Mihai Pop,2 Niranjan Nagarajan,2 David H. Figurski,3 Daniel H. Fine,4 Jeffrey B. Kaplan,4 and Paul J. Planet1,3,5

Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street at Central Park West, New York, New York 10024,1 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742,2 Department of Microbiology, Columbia University, College of Physicians & Surgeons, New York, New York 10032,3 Department of Oral Biology, New Jersey Dental School, Newark, New Jersey 07103,4 Department of Pediatrics, Children's Hospital of New York, Columbia University, College of Physicians and Surgeons, New York, New York 100325

Received 1 April 2009/ Accepted 5 May 2009

ABSTRACT

We report the finished and annotated genome sequence of Aggregatibacter aphrophilus strain NJ8700, a strain isolated from the oral flora of a healthy individual, and discuss characteristics that may affect its dual roles in human health and disease. This strain has a rough appearance, and its genome contains genes encoding a type VI secretion system and several factors that may participate in host colonization.

Aggregatibacter aphrophilus (formerly Haemophilus aphrophilus) (11) is well known as an etiologic agent in infectious endocarditis caused by gram-negative bacteria (7). Most often, however, it is found as a nonpathogenic, commensal resident of dental plaque and the oropharyngeal flora. The complete genome sequence of A. aphrophilus NJ8700 was achieved using a hybrid approach of a shotgun sequencing strategy combined with 454 pyrosequencing (two runs). The 454 sequences were assembled with the Newbler assembler (454 Life Sciences), and the Sanger reads were added to the resulting contigs using MUMmer (8) and custom scripts. The contigs were linked together into scaffolds using Bambus (15), and gaps between contigs were closed by direct sequencing using a technique described by N. Nagarajan et al. (submitted for publication), achieving a 25-fold coverage. Automated annotation was done at the Institute for Genomic Research/J. Craig Venter Institute through the Annotation Engine Service.

The A. aphrophilus NJ8700 genome is 2,313,035 bp in length, with a GC content of 42.23% and 2,320 predicted coding sequences. Approximately 88.4% of nucleotides are predicted to encode proteins. The genome contains 57 tRNAs, including one gene for tRNASec (AAP_1961), and five rRNA nontandem cistrons. Like other Pasteurellaceae (3, 4), the genome has four RNA subunit genes (rpoA, rpoB, rpoC, and rpoZ; AAP_2188, AAP_1813, AAP_1812, and AAP_1427), and five sigma factor genes (AAP_1594, AAP_1967, AAP_2019, AAP_2021, and AAP_2324).

The A. aphrophilus NJ8700 genome contains genes encoding a type VI secretion system (T6SS) (AAP_1851 to -1862, AAP_2123), which is the first instance of its presence in a member of the Pasteurellaceae (1, 2, 9, 10, 16, 17, 20). There are several open reading frames (ORFs) similar to vgrG (AAP_0259, AAP_0279 to -0281, AAP_0288, AAP_292, AAP_1540, AAP_1541, AAP_2121) that encode other possible substrates. The flp-tad cluster (AAP_0177 to -0190) is similar to the tad locus involved in the rough colony phenotype in Aggregatibacter actinomycetemcomitans (12, 13, 14, 21). Also present is a locus required for the assembly of type IVa pili, including pilF, pilA, pilB, pilC, and pilD (AAP_0008, AAP_1464 to -1467). The A. aphrophilus genome contains genes encoding several adhesins that may participate in host colonization (EmaA, AAP_0065; Aae, AAP_0152; YadA and Hia, AAP_0523 and AAP_0527).

Genes for the production of PGA (poly-N-acetylglucosamine), i.e., hmsD, pgaC, pgaB, and pgaA (AAP_1678 to -1681); N-acetylneuraminate lyase (nanA, AAP_A0548); and the dspB enzyme that degrades PGA (AAP_0383 and AAP_0384), all implicated in biofilm formation, are present (6).

A. aphrophilus NJ8700 has several loci implicated in iron utilization, including one for a predicted hemoglobin binding protein, hgpA (AAP_1269), and a hemoglobin/transferrin binding receptor (AAP_2099). Genes for the hemophore receptor HasR (AAP_1311) and a heme utilization protein (AAP_2308) are present. A gene for the TbpA (transferrin binding protein; AAP_1194, AAP_1226) may signal an ability to use transferrin. A. aphrophilus carries genes encoding potential siderophore receptors (AAP_0347, AAP_0905), a TonB-dependent hemoglobin/transferrin/lactoferrin family receptor (AAP_1145), and a receptor for ferrienterochelin/colicins (AAP_1677). Two ORFs may encode chelatin transporters (AAP_1146 to -1149; AAP_783 to -785), along with the ferric-dicitrate transport system (fecBCDE, AAP_1294 to-1297). The genome harbors the genes coding for the Fur regulator (AAP_0360) and periplasmic-binding transport systems: the afe locus (AAP_0393, AAP_0395 to -0397), the hit locus (AAP_1640, AAP_1644 to -1654), and afu loci (AAP_0695 to -0697, AAP_1193 to -1196) (5, 18, 19, 22).

There are three regions of the bacterial chromosome where phage/prophage gene clusters were identified, including the accA-GMP gene intergenic region (acetyl coenzyme A carboxylase, AAP_0460; GMP synthase, AAP_0517), which harbors a prophage (M. Di Bonaventura et al., submitted for publication).

Nucleotide sequence accession number.

The complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus strain NJ8700 has been assigned GenBank accession number CP001607.

ACKNOWLEDGMENTS

We thank the Sackler Institute for Comparative Genomics at the American Museum of Natural History for continued support during this project. This genome sequencing project was supported by funding from the Department of Energy.


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FOOTNOTES
 
* Corresponding author. Mailing address: Sackler Institute for Comparative Genetics, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024. Phone: (212) 769-5670. Fax: 212-769-5277. E-mail: desalle{at}amnh.org Back

FOOTNOTES

{triangledown} Published ahead of print on 15 May 2009. Back

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Journal of Bacteriology, July 2009, p. 4693-4694, Vol. 191, No. 14
0021-9193/09/$08.00+0     doi:10.1128/JB.00447-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.




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