Complete Genome Sequence of Bifidobacterium dentium Strain JCM 1195
 T
 , Isolated from Human Dental Caries

Toh, Y.; Hayashi, Jun; Oshima, Koichiro; Nakano, Akiko; Takayama, Yukiko; Takanashi, Kageyasu; Hattori, Masahira

doi:10.1128/genomea.00284-15

Genome Announc

2015

DOI: 10.1128/genomea.00284-15

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Complete Genome Sequence of Bifidobacterium dentium Strain JCM 1195 ^T , Isolated from Human Dental Caries

Y. Toh

Jun Hayashi

Koichiro Oshima

et al.

Abstract: Bifidobacterium dentium strain JCM 1195T was isolated from human dental caries. Here, we report the complete genome sequence of this organism.

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Cited by 6 publications

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“…In this study, we identified the gene for a difructose-anhydride synthase from the genome of Bifidobacterium dentium isolated from human dental caries ( 27 ). Based on biochemical characterization, X-ray protein crystallography, and computational analysis, we propose a plausible reaction mechanism for the enzyme and the establishment of a novel GH family.…”

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Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family

Kashima

Okumura

Ishiwata

et al. 2021

Journal of Biological Chemistry

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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mentioning

confidence: 99%

Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family

Kashima

Okumura

Ishiwata

et al. 2021

Journal of Biological Chemistry

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Structure of a Core Promoter in Bifidobacterium longum NCC2705

et al. 2020

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Bacterial promoters consist of core sequence motifs termed –35 and –10 boxes. The consensus motifs are TTGACA and TATAAT, respectively, which were identified from leading investigations on Escherichia coli. However, the consensus sequences are not likely to fit genetically divergent bacteria. The sigma factor of the genus Bifidobacterium has a characteristic polar domain in the N terminus, suggesting the possibility of specific promoter recognition. We reevaluated the structure of Bifidobacterium longum NCC2705 promoters and compared them to other bacteria. Transcriptional start sites (TSSs) of the B. longum NCC2705 strain were identified using transcriptome sequencing (RNA-Seq) analysis to extract promoter regions. Conserved motifs of a bifidobacterial promoter were determined using regions upstream of TSSs and a hidden Markov model. As a result, consensus motifs of the –35 and –10 boxes were TTGTGC and TACAAT, respectively. To assess each base of both motifs, we constructed 37 plasmids based on pKO403-TPCTcon, including the hup promoter connected with a chloramphenicol acetyltransferase as a reporter gene. This reporter assay showed two optimal motifs of the –35 and –10 boxes, namely, TTGNNN and TANNNT, respectively. We further analyzed spacer lengths between the –35 and –10 boxes via a bioinformatics approach. The spacer lengths predominant in bacteria have been generally reported to be approximately 17 bp. In contrast, the predominant spacer lengths in the genus Bifidobacterium and related species were 11 bp, in addition to 17 bp. A reporter assay to assess the spacer lengths indicated that the 11-bp spacer length produced unusually high activity. IMPORTANCE The structures of sigma factors vary among bacterial strains, indicating that recognition rules may also vary. Therefore, we investigated the promoter structure of Bifidobacterium longum NCC2705 using a bioinformatics approach and wet analyses. The most frequent and optimal motifs were similar to other bacterial consensus motifs. The optimal spacer length between the two boxes was reported to be 17 bp. It is widely applied to a bioinformatics approach for other bacteria. Unexpectedly, conserved spacer lengths were 11 bp as well as 17 bp in the genus Bifidobacterium. Moreover, the sigma factor of the genus Bifidobacterium has a characteristic domain in the N terminus which may contribute to the additional functions. Hence, it would be valuable to reevaluate the promoter in other organisms.

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Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species

Zafar

Saier

2021

Microb Physiol

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The human microbiome influences human health in both negative and positive ways. Studies on the transportomes of these organisms yield information that may be utilized for various purposes, including the identification of novel drug targets and the manufacture of improved probiotic strains. Moreover, these genomic analyses help to improve our understanding of the physiology and metabolic capabilities of these organisms. The present study is a continuation of our studies on the transport proteins of the major gut microbes. Bifidobacterium species are essential members of the human gut microbiome, and they initiate colonization of the gut at birth, providing health benefits that last a lifetime. In this study we analyze the transportomes of nine bifidobacterial species: B. adolescentis, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. longum subsp. infantis, B. longum subsp. longum, and B. pseudocatenulatum. All of these species have proven probiotic characteristics and exert beneficial effects on human health. Surprisingly, we found that all nine of these species have similar pore-forming toxins and drug exporters that may play roles in pathogenesis. These species have transporters for amino acids, carbohydrates, and proteins, essential for their organismal lifestyles and adaption to their respective ecological niches. The strictly probiotic species, B. bifidum, however, contains fewer such transporters, thus indicative of limited interactions with host cells and other gut microbial counterparts. The results of this study were compared with those of our previous studies on the transportomes of multiple species of Bacteroides, Escherichia coli/Salmonella, and Lactobacillus. Overall, bifidobacteria have larger transportomes (based on percentages of total proteins) than the previously examined groups of bacterial species, with a preference for primary active transport systems over secondary carriers. Taken together, these results provide useful information about the physiologies and pathogenic potentials of these probiotic organisms as reflected by their transportomes.

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Complete Genome Sequence of Bifidobacterium dentium Strain JCM 1195 ^T , Isolated from Human Dental Caries

Abstract: Bifidobacterium dentium strain JCM 1195T was isolated from human dental caries. Here, we report the complete genome sequence of this organism.

Cited by 6 publications

References 10 publications

Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family

Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family

Structure of a Core Promoter in Bifidobacterium longum NCC2705

Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine <b><i>Bifidobacterium</i></b> Species

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Complete Genome Sequence of Bifidobacterium dentium Strain JCM 1195 T , Isolated from Human Dental Caries

Abstract: Bifidobacterium dentium strain JCM 1195T was isolated from human dental caries. Here, we report the complete genome sequence of this organism.

Cited by 6 publications

References 10 publications

Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family

Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family

Structure of a Core Promoter in Bifidobacterium longum NCC2705

Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine <b><i>Bifidobacterium</i></b> Species

Contact Info

Product

Resources

About

Complete Genome Sequence of Bifidobacterium dentium Strain JCM 1195 ^T , Isolated from Human Dental Caries