Analysis of a Band 7/MEC-2 Family Gene of <i>Porphyromonas                   gingivalis</i>

Walters, Sheila; Rodrigues, Paulo Henrique Mazza; Bélanger, Myriam; Whitlock, Joan A.; Progulske‐Fox, Ann

doi:10.1177/0022034508328381

Cited by 8 publications

(11 citation statements)

References 25 publications

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“…Several of the recorded TARs were previously verified as operons in P. gingivalis, such as the locus containing the genes PG1333 to PG1335 in strain W83 (82) and the htrABCD locus (PG0645 to PG0648) (68) and the rag locus (PG0185-PG0186) (26) in strain W50. Johnson et al (35) recently reported the transcriptional start site of the bcp-recA-vimA-vimE-vimF operon in P. gingivalis W83 to be located at the genomic position nt 942713, downstream from the start of the current CMR-JCVI/LANL-annotated bcp gene.…”

Section: Discussionmentioning

confidence: 94%

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: 94%

Comprehensive Transcriptome Analysis of the Periodontopathogenic Bacterium Porphyromonas gingivalis W83

Høvik

Yu²,

Olsen

et al. 2012

J Bacteriol

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“…We did observe that FnrL does indirectly repress a siderophore ABC transporter ( rcc02116 ), a FeoA family protein ( rcc02028 ), a Fe(III) type ABC transporter ( rcc02579 ) and FeoA2 that codes for a ferrous iron transporter ( rcc00091 ) (Additional file 2 : Table S2). One of the highest enriched (21-fold) sites was found in one uncharacterized set of genes ( rcc3401 - rcc3402 ) the first of which is a band 7/SPFH family protein thought to be the core of an ion channel while the second is a hypothetical protein that shares 24 % identity to a membrane protease found to be important for virulence in P. gingivalis W83 [ 25 ]. These two genes are typically found in an operon and appear to form the foundation of an ion channel.…”

Section: Resultsmentioning

confidence: 99%

Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli

Kumka

Bauer

2015

BMC Genomics

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BackgroundFNR homologues constitute an important class of transcription factors that control a wide range of anaerobic physiological functions in a number of bacterial species. Since FNR homologues are some of the most pervasive transcription factors, an understanding of their involvement in regulating anaerobic gene expression in different species sheds light on evolutionary similarity and differences. To address this question, we used a combination of high throughput RNA-Seq and ChIP-Seq analysis to define the extent of the FnrL regulon in Rhodobacter capsulatus and related our results to that of FnrL in Rhodobacter sphaeroides and FNR in Escherichia coli.ResultsOur RNA-seq results show that FnrL affects the expression of 807 genes, which accounts for over 20 % of the Rba. capsulatus genome. ChIP-seq results indicate that 42 of these genes are directly regulated by FnrL. Importantly, this includes genes involved in the synthesis of the anoxygenic photosystem. Similarly, FnrL in Rba. sphaeroides affects 24 % of its genome, however, only 171 genes are differentially expressed in common between two Rhodobacter species, suggesting significant divergence in regulation.ConclusionsWe show that FnrL in Rba. capsulatus activates photosynthesis while in Rba. sphaeroides FnrL regulation reported to involve repression of the photosystem. This analysis highlights important differences in transcriptional control of photosynthetic events and other metabolic processes controlled by FnrL orthologues in closely related Rhodobacter species. Furthermore, we also show that the E. coli FNR regulon has limited transcriptional overlap with the FnrL regulons from either Rhodobacter species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2162-4) contains supplementary material, which is available to authorized users.

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“…Interestingly, PG1334, the middle gene of the operon in W83, was identified in an in vivo-induced antigen technology (IVIAT) study as a gene that is induced in vivo during human periodontitis (50). Subsequent quantitative RT-PCR studies by Walters et al confirmed that the PG1334 transcript is detected more frequently in dental plaque samples from periodontal disease sites than from healthy sites after taking into account P. gingivalis abundance, consistent with induction of expression during disease (49).…”

Section: Resultsmentioning

confidence: 88%

Identification of PGN_1123 as the Gene Encoding Lipid A Deacylase, an Enzyme Required for Toll-Like Receptor 4 Evasion, in Porphyromonas gingivalis

et al. 2019

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Removal of one acyl chain from bacterial lipid A by deacylase activity is a mechanism used by many pathogenic bacteria to evade the host's Toll-like receptor 4 (TLR4)-mediated innate immune response. In Porphyromonas gingivalis, a periodontal pathogen, lipid A deacylase activity converts a majority of the initially synthesized penta-acylated lipid A, a TLR4 agonist, to tetra-acylated structures, which effectively evade TLR4 sensing by being either inert or antagonistic at TLR4. In this paper, we report successful identification of the gene that encodes the P. gingivalis lipid A deacylase enzyme. This gene, PGN_1123 in P. gingivalis 33277, is highly conserved within P. gingivalis, and putative orthologs are phylogenetically restricted to the Bacteroidetes phylum. Lipid A of ΔPGN_1123 mutants is penta-acylated and devoid of tetra-acylated structures, and the mutant strain provokes a strong TLR4-mediated proinflammatory response, in contrast to the negligible response elicited by wild-type P. gingivalis. Heterologous expression of PGN_1123 in Bacteroides thetaiotaomicron promoted lipid A deacylation, confirming that PGN_1123 encodes the lipid A deacylase enzyme. IMPORTANCE Periodontitis, commonly referred to as gum disease, is a chronic inflammatory condition that affects a large proportion of the population. Porphyromonas gingivalis is a bacterium closely associated with periodontitis, although how and if it is a cause for the disease are not known. It has a formidable capacity to dampen the host's innate immune response, enabling its persistence in diseased sites and triggering microbial dysbiosis in animal models of infection. P. gingivalis is particularly adept at evading the host's TLR4-mediated innate immune response by modifying the structure of lipid A, the TLR4 ligand. In this paper, we report identification of the gene encoding lipid A deacylase, a key enzyme that modifies lipid A to TLR4-evasive structures.

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Analysis of a Band 7/MEC-2 Family Gene of Porphyromonas gingivalis

Cited by 8 publications

References 25 publications

Comprehensive Transcriptome Analysis of the Periodontopathogenic Bacterium Porphyromonas gingivalis W83

Comprehensive Transcriptome Analysis of the Periodontopathogenic Bacterium Porphyromonas gingivalis W83

Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli

Identification of PGN_1123 as the Gene Encoding Lipid A Deacylase, an Enzyme Required for Toll-Like Receptor 4 Evasion, in Porphyromonas gingivalis

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