DOI: 10.6084/m9.figshare.12782576.v4
title: Characterization of human genes modulated by Porphyromonas gingivalis highlights the ribosome, hypothalamus, and cholinergic neurons

description: <i>Porphyromonas gingivalis</i>, a bacterium associated with periodontal disease, is a suspected cause of Alzheimer’s disease. This bacterium is reliant on gingipain proteases, which cleave host proteins after arginine and lysine residues. To characterize gingipain susceptibility, we performed enrichment analyses of arginine and lysine proportion proteome-wide. Genes differentially expressed in brain samples with detected <i>P. gingivalis</i> reads were also examined. Genes from these analyses were tested for functional enrichment and specific neuroanatomical expression patterns. Proteins in the SRP-dependent cotranslational protein targeting to membrane pathway were enriched for these residues and previously associated with periodontal and Alzheimer’s disease. These ribosomal genes are up-regulated in prefrontal cortex samples with detected <i>P. gingivalis</i> sequences. Other differentially expressed genes have been previously associated with dementia (ITM2B, MAPT, ZNF267, and DHX37). For an anatomical perspective, we characterized the expression of the <i>P. gingivalis</i> associated genes in the mouse and human brain. This analysis highlighted the hypothalamus, cholinergic neurons, and the basal forebrain. Our results suggest markers of neural <i>P. gingivalis</i> infection and link the cholinergic and gingipain hypotheses of Alzheimer’s disease. <br>Code on github: https://github.com/leonfrench/gingipain_release<br>Supplement Table 1: Proteome-wide arginine and lysine counts and proportion.<br>Supplement Table 2: Gene Ontology enrichment results for arginine and lysine proportions.<br>Supplement Table 3: SRP-dependent cotranslational protein targeting to membrane amino acid specificity tests. <br>Supplement Table 4: Results of differential expression tests for P. gingivalis detection.<br>Supplement Table 5: Gene Ontology enrichment results for genes associated with P. gingivalis detection.<br>Supplement Table 6: Neuroanatomical enrichment results for genes associated with P. gingivalis detection.<br>Supplement Table 7: Nervous system cell-type enrichment results for genes associated with P. gingivalis detection.<br>Supplement Table 8: Neuroanatomical enrichment results for the SRP-dependent cotranslational protein targeting to membrane genes.<br>Supplement Table 9: Nervous system cell-type enrichment results for the SRP-dependent cotranslational protein targeting to membrane genes.<br>Supplement Figure 1: Gingipain digestion of 70S ribosomes. Fifteen microliter reactions containing 2.5 ug of 70S ribosome and either 120 nM of recombinant Lys-gingipain (rKgp), Arg-gingipains (rRgpA and rRgpB), or about 206 – 412 µM (one unit in a 15 µL reaction volume) of Caspase-3 were incubated at 30°C for 1 h or 3 h. After incubation, results were visualized using SDS PAGE & Coomassie brilliant blue staining. The Precision Plus Protein WesternC Dual Color ladder was used for band sizing. The asterisk (*) to the left of the ribosome only control indicates a faint band present at about 60 kDa. This faint band appeared to be digested by Kgp and RgpB after 1 and 3 hours of incubation, as indicated by carets (^) to the left of the Kgp and RgpB.<br>