Comparative transcriptomic analysis of Porphyromonas gingivalis biofilm and planktonic cells

Abstract

Background: Porphyromonas gingivalis in subgingival dental plaque, as part of a mature biofilm, has been strongly implicated in the onset and progression of chronic periodontitis. In this study using DNA microarray we compared the global gene expression of a P. gingivalis biofilm with that of its planktonic counterpart grown in the same continuous culture.

Results: Approximately 18% (377 genes, at 1.5 fold or more, P-value < 0.01) of the P. gingivalis genome was differentially expressed when the bacterium was grown as a biofilm. Genes that were down-regulated in biofilm cells, relative to planktonic cells, included those involved in cell envelope biogenesis, DNA replication, energy production and biosynthesis of cofactors, prosthetic groups and carriers. A number of genes encoding transport and binding proteins were up-regulated in P. gingivalis biofilm cells. Several genes predicted to encode proteins involved in signal transduction and transcriptional regulation were differentially regulated and may be important in the regulation of biofilm growth.

Conclusion: This study analyzing global gene expression provides insight into the adaptive response of P. gingivalis to biofilm growth, in particular showing a down regulation of genes involved in growth and metabolic activity.

Figure 1

Correlation between microarray and real-time PCR. Correlation between microarray and real-time-PCR gene expression ratios determined for biofilm versus planktonic cells. The log₂-transformed microarray and real-time-PCR ratios were used to determine the Spearman Rank correlation coefficient (r = 0.86, p < 0.01).

Figure 2

Genes differently expressed in P. gingivalis W50 biofilm. Genes differentially expressed in P. gingivalis W50 biofilm cells relative to planktonic cells (1.5 fold or more, P-value < 0.01) grouped by TIGR functional role categories. A, amino acid biosynthesis; B, biosynthesis of cofactors, prosthetic groups, and carriers; C, cell envelope; D, cellular processes; E, central intermediary metabolism; F, DNA metabolism; G, disrupted reading frame; H, energy metabolism; I, fatty acid and phospholipid metabolism; J, mobile and extrachromosomal element functions; K, protein fate; L, protein synthesis; M, purines, pyrimidines, nucleosides and nucleotides; N, regulatory functions; O, signal transduction; P, transcription; Q, transport and binding proteins; R, unknown function; and S, hypothetical or conserved hypothetical proteins.