Application of rpoB and zinc protease gene for use in molecular discrimination of Fusobacterium nucleatum subspecies.
Fusobacterium nucleatum is classified into five subspecies that inhabit the human oral cavity (F. nucleatum subsp. nucleatum, F. nucleatum subsp. polymorphum, F. nucleatum subsp. fusiforme, F. nucleatum subsp. vincentii, and F. nucleatum subsp. animalis) based on several phenotypic characteristics and DNA-DNA hybridization patterns. However, the methods for detecting or discriminating the clinical isolates of F. nucleatum at the subspecies levels are laborious, expensive, and time-consuming. Therefore, in this study, the nucleotide sequences of the RNA polymerase beta-subunit gene (rpoB) and zinc protease gene were analyzed to discriminate the subspecies of F. nucleatum. The partial sequences of rpoB (approximately 2,419 bp), the zinc protease gene (878 bp), and 16S rRNA genes (approximately 1,500 bp) of the type strains of five subspecies, 28 clinical isolates of F. nucleatum, and 10 strains of F. periodonticum (as a control group) were determined and analyzed. The phylogenetic data showed that the rpoB and zinc protease gene sequences clearly delineated the subspecies of F. nucleatum and provided higher resolution than the 16S rRNA gene sequences in this respect. According to the phylogenetic analysis of rpoB and the zinc protease gene, F. nucleatum subsp. vincentii and F. nucleatum subsp. fusiforme might be classified into a single subspecies. Five clinical isolates could be delineated as a new subspecies of F. nucleatum. The results suggest that rpoB and the zinc protease gene are efficient targets for the discrimination and taxonomic analysis of the subspecies of F. nucleatum.
Kim
Hwa-Sook
HS
Department of Oral Biochemistry, School of Dentistry, Chosun University, 375 Dong-Gu, Seosuk-Dong, Gwangju 501-759, Republic of Korea.
Lee
Dae-Sil
DS
Chang
Young-Hyo
YH
Kim
Min Jung
MJ
Koh
Sukhoon
S
Kim
Joongsu
J
Seong
Jin-Hyo
JH
Song
Soo Keun
SK
Shin
Hwan Seon
HS
Son
Jae-Beum
JB
Jung
Min Young
MY
Park
Soon-Nang
SN
Yoo
So Young
SY
Cho
Ki Woon
KW
Kim
Dong-Kie
DK
Moon
Seonghoon
S
Kim
Dooil
D
Choi
Yongseok
Y
Kim
Byung-Ock
BO
Jang
Hyun-Seon
HS
Kim
Chun Sung
CS
Kim
Chan
C
Choe
Son-Jin
SJ
Kook
Joong-Ki
JK
D001426:Bacterial Proteins / Q000235:genetics*; D015373:Bacterial Typing Techniques; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D005674:Fusobacterium Infections / Q000382:microbiology; D016967:Fusobacterium nucleatum / Q000145:classification* / Q000235:genetics*; D005838:Genotype; D006801:Humans; D008666:Metalloendopeptidases / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D017422:Sequence Analysis, DNA
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit; D008666:Metalloendopeptidases