Characterization of the Novel
            <i>Fusobacterium nucleatum</i>
            Plasmid pKH9 and Evidence of an Addiction System

Bachrach, Gilad; Haake, Susan Kinder; Glick, Alon; Hazan, Ronen; Naor, Ronit; Andersen, R N; Kolenbrander, Paul E.

doi:10.1128/aem.70.12.6957-6962.2004

Cited by 24 publications

(18 citation statements)

References 28 publications

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“…The A rea R equired for R eplication in a P lasmid O f F usobacterium (ARRPOF) motif ( Supplementary Figure S3 ) occurs in Fusobacterium nucleatum plasmid pKH9. Although this plasmid has a predicted rep (replication) gene, which presumably can replicate the plasmid, the plasmid can also replicate when the rep gene is deleted ( 56 ). A 1 Kb region that lacks predicted genes ( Supplementary Text ) was found to be sufficient for replication ( 56 ).…”

Section: Resultsmentioning

confidence: 99%

“…Although this plasmid has a predicted rep (replication) gene, which presumably can replicate the plasmid, the plasmid can also replicate when the rep gene is deleted ( 56 ). A 1 Kb region that lacks predicted genes ( Supplementary Text ) was found to be sufficient for replication ( 56 ). This region was cut into two, and each sub-region individually failed to allow replication.…”

Section: Resultsmentioning

confidence: 99%

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Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

Weinberg

Lünse

Corbino

et al. 2017

Nucleic Acids Research

128

216

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The discovery of structured non-coding RNAs (ncRNAs) in bacteria can reveal new facets of biology and biochemistry. Comparative genomics analyses executed by powerful computer algorithms have successfully been used to uncover many novel bacterial ncRNA classes in recent years. However, this general search strategy favors the discovery of more common ncRNA classes, whereas progressively rarer classes are correspondingly more difficult to identify. In the current study, we confront this problem by devising several methods to select subsets of intergenic regions that can concentrate these rare RNA classes, thereby increasing the probability that comparative sequence analysis approaches will reveal their existence. By implementing these methods, we discovered 224 novel ncRNA classes, which include ROOL RNA, an RNA class averaging 581 nt and present in multiple phyla, several highly conserved and widespread ncRNA classes with properties that suggest sophisticated biochemical functions and a multitude of putative cis-regulatory RNA classes involved in a variety of biological processes. We expect that further research on these newly found RNA classes will reveal additional aspects of novel biology, and allow for greater insights into the biochemistry performed by ncRNAs.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

Weinberg

Lünse

Corbino

et al. 2017

Nucleic Acids Research

128

216

View full text Add to dashboard Cite

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“…The two shuttle vectors developed for fusobacteria (58)(59)(60) and the sequencing and annotation of three strains representing subspecies F. nucleatum subsp. nucleatum, Fusobacterium nucleatum subsp.…”

Section: Figmentioning

confidence: 99%

Fap2 of Fusobacterium nucleatum Is a Galactose-Inhibitable Adhesin Involved in Coaggregation, Cell Adhesion, and Preterm Birth

et al. 2015

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Fusobacterium nucleatum is a common oral anaerobe involved in periodontitis that is known to translocate and cause intrauterine infections. In the oral environment, F. nucleatum adheres to a large diversity of species, facilitating their colonization and creating biological bridges that stabilize the multispecies dental biofilm. Many of these interactions (called coadherences or coaggregations) are galactose sensitive. Galactose-sensitive interactions are also involved in the binding of F. nucleatum to host cells. Hemagglutination of some F. nucleatum strains is also galactose sensitive, suggesting that a single galactose-sensitive adhesin might mediate the interaction of fusobacteria with many partners and targets. In order to identify the fusobacterial galactose-sensitive adhesin, a system for transposon mutagenesis in fusobacteria was created. The mutant library was screened for hemagglutination deficiency, and three clones were isolated. All three clones were found to harbor the transposon in the gene coding for the Fap2 outer membrane autotransporter. The three fap2 mutants failed to show galactose-inhibitable coaggregation with Porphyromonas gingivalis and were defective in cell binding. A fap2 mutant also showed a 2-log reduction in murine placental colonization compared to that of the wild type. Our results suggest that Fap2 is a galactose-sensitive hemagglutinin and adhesin that is likely to play a role in the virulence of fusobacteria.

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“…Our finding that pFN1-like relaxases are more prevalent in F. nucleatum than detectable plasmids may in some instances reflect integration of plasmid elements into the bacterial chromosome. Additional hybridization studies using sequences from other fusobacterial plasmids such as pFN3 (Haake et al, 2000; Karpathy et al, 2007) and pKH9 (Bachrach et al, 2004) may indicate more extensive prevalence of plasmid-related sequences in this species.…”

Section: Discussionmentioning

confidence: 99%

“…The first report of plasmids from F. nucleatum indicated that plasmids or plasmid-related sequences were found in 18% of the oral isolates examined (McKay et al, 1995). Plasmids isolated from F. nucleatum are reported to range from 5 to 15 kb (Bachrach et al, 2004; Haake et al, 2000; McKay et al, 1995), which is insufficient to encode all the genes needed for conjugation of self-transmissible plasmids. However, sequence analyses of several F. nucleatum plasmids revealed homologues of plasmid relaxases suggesting that the plasmids may be mobilizable with conjugative functions provided in trans (Haake et al, 2000; Karpathy et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Mobilization and prevalence of a fusobacterial plasmid

Claypool

Yoder

Citron³

et al. 2010

Plasmid

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Fusobacterium nucleatum is a Gram-negative anaerobic rod found in dental plaque biofilms, and is an opportunistic pathogen implicated in periodontitis as well as a wide range of systemic abscesses and infections. Genomic analyses of F. nucleatum indicate considerable genetic diversity and a prominent role for horizontal gene transfer in the evolution of the species. Several plasmids isolated from F. nucleatum, including pFN1, harbor relaxase gene homologues that may function in plasmid mobilization. In this investigation we examined the RP4-mediated mobilization properties of pFN1 and the prevalence of pFN1-related sequences in a panel of F. nucleatum clinical isolates. The fusobacterial plasmid pFN1 was mobilized by RP4 at a high frequency. Deletion analyses were used to delineate the core mobilon of pFN1, which consisted of the relaxase gene (rlx), an upstream open reading frame ORF4 and a region of DNA upstream of ORF4 with potential nic sites. To examine the prevalence of pFN1 in a panel of clinical isolates, total DNA isolated from the strains was hybridized with pFN1 replication (repA) and rlx gene probes. DNA from strains harboring plasmids known to be homologous to pFN1 hybridized with both the repA and rlx probes. Five additional strains were rlx-positive but repA-negative, indicating a greater prevalence of rlx-related genes in comparison with repA-related genes. Plasmid or plasmid-related sequences were identified in 11.5% of the strains examined. These findings demonstrate mobilization properties of a fusobacterial plasmid that may be important in horizontal gene transfer.

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Characterization of the Novel Fusobacterium nucleatum Plasmid pKH9 and Evidence of an Addiction System

Cited by 24 publications

References 28 publications

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

Fap2 of Fusobacterium nucleatum Is a Galactose-Inhibitable Adhesin Involved in Coaggregation, Cell Adhesion, and Preterm Birth

Mobilization and prevalence of a fusobacterial plasmid

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