Comprehensive Transcriptome Analysis of the Periodontopathogenic Bacterium Porphyromonas gingivalis W83

Abstract

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.

Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis

“…performed RNA-seq analysis of mRNA expression by P. gingivalis strain W83 from which 455 of the possible 463 ATCC 33277 essential genes were assayed [53]. This analysis demonstrated that 452 of 455 P. gingivalis ATCC 33277 essential genes were expressed during growth on blood agar medium (Additional file 1: Table S1).…”

Comparative gene expression analysis of Porphyromonas gingivalis ATCC 33277 in planktonic and biofilms states

“…Furthermore, the CRISPR-Cas and associated CAS proteins system represents a unique system that provides prokaryotic cells, as P . gingivalis , adaption and protection from host defenses [54, 55]. Down-regulation of the genes PGN_1924-Cas2, PGN_1925-Cas1 may suggest a decrease in the defensive capability of P .…”

Identification and Characterization of Prokaryotic Dipeptidyl-peptidase 5 from Porphyromonas gingivalis

“…The bacterium does not ferment carbohydrates, but grows under strict anaerobic conditions using proteinaceous substrates as carbon and energy sources. Although anaerobic energy production in P. gingivalis is poorly understood, biochemical examinations (7,8), whole genome information (9,10), and transcriptome analysis (11) have led to drafts of the configurations of the entire metabolism and transport pathways.…”