Gene expression changes in Porphyromonas gingivalis W83 after inoculation in rat oral cavity

Chronic periodontitis is initiated by periodontal pathogens, including P.gingivalis. Our study showed that P.gingivalis W83 induced rat gingival tissue inflammation, and alveolar bone loss, which is the
key feature of periodontitis. Therefore, our study demonstrates that P.gingivalis W83 has pathogenic effects on rat oral cavity. After inoculation in rat oral cavity
for 8 weeks, P.gingivalis W83 were isolated, and analyzed by microarray. In the detected 1786 genes, 42 genes
were upregulated, whereas 22 genes were downregulated, indicating that the local periodontal
environment can change the gene expression profile of P.gingivalis W83.

In the 42 upregulated genes, 30 expressed hypothetical proteins. Among other 12 genes,
PG0874, PG0009, PG0427, PG0942 and PG0590 are in the same class in JCVI cell function classification. They all function as
mobile extrachromosomal factor: transposon. Transposon is a removable genome DNA sequence,
which can “jump” in genome from one location to another through the process of cutting
and integration. Transposition is generally known to be triggered by cellular stress
12]–14], therefore upregulation of these transposons suggests that P.gingivalis W83 inoculated in rat oral cavity may adapt local environment for its own survival,
which is consistent with some other studies 15],16].

In the 22 downregulated genes, 7 genes encode transport and binding proteins. All
these proteins are involved in cell transmembrane transportation. They can transport
many substrates, such as metabolites, ion, sugar, amino acids, lipids, cholesterol
and drugs 17]. PG2008 encodes a TonB dependent receptor protein, responsible for iron transmembrane transportation
18]. As iron ion is necessary for the breeding and spreading of P.gingivalis W83, downregulation of PG2008 suggests the subdued iron transferring and proliferation of P.gingivalis W83. There are 4 downregulated genes encoding proteins related to nucleic acid and
protein metabolism. PG1129 encodes a nucleotide reductase, which is related to purine, pyrimidine, nucleotide
and DNA metabolism, and plays a regulating role in cell proliferation. Products of
PG1993 and PG0001 are related to the metabolism of DNA, such as copy, restructuring and repair. Therefore,
downregulation of these genes means that the proliferation of inoculated P.gingivalis W83 is in certain obstacles.

PG1042 encodes a putative glycogen synthase, involved in biosynthesis and degradation of
polysaccharides. Downregulation of PG1042 suggests a disturbed energy metabolism. PG0141 encodes a spoOJ protein related to cell division, and PG1975 encodes hemagglutinin HagC related to pathogenicity of P.gingivalis W83. In addition, PG1982 encodes a CRISPR protein related to CAS1 family. CRISPR/CAS system can protect bacteria
against the encroachment by phage, and resist other chromosome genetic material and
prevent from the expression of their genes 19]–21]. Downregulation of PG1982 suggests a decrease in the defense capability of P.gingivalis W83.

It should be noted that gene expression observed in this study was in mRNA level.
As we have known, alterations in mRNA expression are not always consistent with those
in protein expression. Therefore, observations in protein level of gene expression
will be more convincing. However, it is impracticable to analyze the protein expression
of all 64 genes with RNA expression alteration. Moreover, some products of these genes
are still hypothetical proteins. Because the inoculated P.gingivalis was cultured outside the rat oral cavity for some days before RNA extraction, the
RNA samples cannot exactly reflect the changes in gene expression after inoculation,
although the results can still indicate which genes are upregulated or downregulated.