The genetic relatedness of <i>Porphyromonas gingivalis</i> clinical and laboratory strains assessed by analysis of insertion sequence (IS) element distribution

Califano, Joseph V.; Arimoto, Takafumi; Kitten, Todd

doi:10.1034/j.1600-0765.2003.00665.x

Cited by 17 publications

(15 citation statements)

References 31 publications

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“…From mapping the distribution of IS elements in several P. gingivalis laboratory strains and clinical isolates, Califano et al (7) suggested a preserved strain relationship reflecting the fact that neither recent transposition nor homologous recombination between IS copies had occurred extensively in the isolates studied. However, Califano et al (7) emphasized that their results do not imply that genomic variation caused by IS elements never occurred or that the transposition between IS elements is not im-portant in adapting to new environments. Evidence of genomic rearrangement has been detected where a gene is interrupted with an IS sequence (45).…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Transcriptome Analysis of the Periodontopathogenic Bacterium Porphyromonas gingivalis W83

Høvik

Yu²,

Olsen

et al. 2012

J Bacteriol

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High-density tiling microarray and RNA sequencing technologies were used to analyze the transcriptome of the periodontopathogenic bacterium Porphyromonas gingivalis. The compiled P. gingivalis transcriptome profiles were based on total RNA samples isolated from three different laboratory culturing conditions, and the strand-specific transcription profiles generated covered the entire genome, including both protein coding and noncoding regions. The transcription profiles revealed various operon structures, 5=-and 3=-end untranslated regions (UTRs), differential expression patterns, and many novel, not-yetannotated transcripts within intergenic and antisense regions. Further transcriptome analysis identified the majority of the genes as being expressed within operons and most 5= and 3= ends to be protruding UTRs, of which several 3= UTRs were extended to overlap genes carried on the opposite/antisense strand. Extensive antisense RNAs were detected opposite most insertion sequence (IS) elements. Pairwise comparative analyses were also performed among transcriptome profiles of the three culture conditions, and differentially expressed genes and metabolic pathways were identified. With the growing realization that noncoding RNAs play important biological functions, the discovery of novel RNAs and the comprehensive transcriptome profiles compiled in this study may provide a foundation to further understand the gene regulation and virulence mechanisms in P. gingivalis. The transcriptome profiles can be viewed at and downloaded from the Microbial Transcriptome Database website, http://bioinformatics.forsyth.org/mtd.

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Section: Discussionmentioning

confidence: 99%

Comprehensive Transcriptome Analysis of the Periodontopathogenic Bacterium Porphyromonas gingivalis W83

Høvik

Yu²,

Olsen

et al. 2012

J Bacteriol

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“…Therefore, we selected 10 transconjugants from a W83Em-33277Tc mating and analyzed these strains by Southern hybridization to determine the extent of genome chimerization. Chromosomal DNA digests were probed with ISPG4, an insertion sequence that has nine copies in W83 and none in 33277 (6). As shown in Fig.…”

Section: Presence Of Type Iv-related Elements In P Gingivalis Strainsmentioning

confidence: 99%

“…Numerous studies have attempted to measure the degree of genetic variability in the P. gingivalis population by using techniques such as pulsed-field gel electrophoresis, restriction fragment length polymorphisms, insertion sequence hybridization, cross-species microarray hybridization, and multilocus sequence typing (2,6,7,10,15,24,27). All studies to date have pointed to significant levels of genetic variation among P. gingivalis strains, indicating that the population structure of these organisms is not strictly clonal but instead is influenced by DNA recombination between different strains.…”

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confidence: 99%

Conjugal Transfer of Chromosomal DNA Contributes to Genetic Variation in the Oral Pathogen Porphyromonas gingivalis

et al. 2007

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Porphyromonas gingivalis is a major oral pathogen that contributes to the development of periodontal disease. There is a significant degree of genetic variation among strains of P. gingivalis, and the population structure has been predicted to be panmictic, indicating that horizontal DNA transfer and recombination between strains are likely. The molecular events underlying this genetic exchange are not understood, although a putative type IV secretion system is present in the genome sequence of strain W83, implying that DNA conjugation may be responsible for genetic transfer in these bacteria. In this study, we provide in vitro evidence for the horizontal transfer of DNA using plasmid-and chromosome-based assays. In the plasmid assays, Bacteroides-derived shuttle vectors were tested for transfer from P. gingivalis strains into Escherichia coli. Of the eight strains tested, five were able to transfer DNA into E. coli by a mechanism most consistent with conjugation. Additionally, strains W83 and 33277 tested positive for the transfer of chromosomally integrated antibiotic resistance markers. Ten chimeras resulting from the chromosomal transfer assay were further analyzed by Southern hybridization and were shown to have exchanged DNA fragments of between 1.1 and 5.6 kb, but the overall strain identity remained intact. Chimeras showed phenotypic changes in the ability to accrete into biofilms, implying that DNA transfer events are sufficient to generate measurable changes in complex behaviors. This ability to transfer chromosomal DNA between strains may be an adaptation mechanism in the complex environment of the host oral cavity.

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“…In multispecies communities such as the dental biofilm, the possibilities for genetic exchange probably increase even more, as there is a constant supply of genetic material released from scores of Gram-positive and Gram-negative species of bacteria. Not surprisingly, many of the sequenced oral bacteria show a plethora of insertion sequences and other evidence of transposition (Califano et al, 2003;Kapatral et al, 2002). This is also true for S. mutans, which contains a variety of loci that appear to have resulted from horizontal gene transfer (Ajdić et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

A unique nine-gene comY operon in Streptococcus mutans

Merritt¹,

Qi²,

Shi³

2005

Microbiology

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Many Gram-positive and Gram-negative bacteria possess natural competence mechanisms for DNA capture and internalization. In Bacillus subtilis, natural competence is absolutely dependent upon the presence of a seven-gene operon known as the comG operon (comGA-G). In species of Streptococcus, this function has been described for a four-gene operon (comYA-D in Streptococcus gordonii and cglA-D in Streptococcus pneumoniae). In this study, a nine-orf operon (named comYA-I) required for natural competence in Streptococcus mutans was identified and characterized. Orf analysis of this operon indicates that the first four Orfs (ComYA-D) share strong homology with ComYA-D of S. gordonii and CglA-D of S. pneumoniae, the fifth to seventh Orfs (ComYE-G) match conserved hypothetical proteins from various species of Streptococcus with ComYF possessing a predicted ComGF domain, the eighth Orf (ComYH) shows a strong homology to numerous DNA methyltransferases from restriction/modification systems, and the ninth Orf (ComYI) is homologous to acetate kinase (AckA). RT-PCR analysis of the orf junctions confirmed that all nine orfs were present in a single transcript, while real-time RT-PCR analysis demonstrated that these orfs were expressed at a level very similar to that of the first orf in the operon. Mutations were constructed in all nine putative orfs. The first seven genes (comYA-G) were found to be essential for natural competence, while comYH and comYI had reduced and normal natural competence ability, respectively. Analyses of S. mutans comY-luciferase reporter fusions indicated that comY expression is growth-phase dependent, with maximal expression at an OD 600 of about 0?2, while mutations in ciaH, comC and luxS reduced the level of comY expression. In addition, comY operon expression appears to be correlated with natural competence ability.

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The genetic relatedness of Porphyromonas gingivalis clinical and laboratory strains assessed by analysis of insertion sequence (IS) element distribution

Cited by 17 publications

References 31 publications

Comprehensive Transcriptome Analysis of the Periodontopathogenic Bacterium Porphyromonas gingivalis W83

Comprehensive Transcriptome Analysis of the Periodontopathogenic Bacterium Porphyromonas gingivalis W83

Conjugal Transfer of Chromosomal DNA Contributes to Genetic Variation in the Oral Pathogen Porphyromonas gingivalis

A unique nine-gene comY operon in Streptococcus mutans

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