Abstract
Bacteroidetes feature prominently in the human microbiome, as major colonizers of the gut and clinically relevant pathogens elsewhere. Here, we reveal a new Bacteroidetes specific feature in the otherwise widely conserved Sec/SPI (Sec translocase/signal peptidase I) pathway. In Bacteroidetes, but not the entire FCB group or related phyla, signal peptide cleavage exposes N-terminal glutamine residues in most SPI substrates. Reanalysis of published mass spectrometry data for five Bacteroidetes species shows that the newly exposed glutamines are cyclized to pyroglutamate (also termed 5-oxoproline) residues. Using the dental pathogen Porphyromonas gingivalis as a model, we identify the PG2157 (also called PG_RS09565, Q7MT37) as the glutaminyl cyclase in this species, and map the catalytic activity to the periplasmic face of the inner membrane. Genetic manipulations that alter the glutamine residue immediately after the signal peptide in the pre-pro-forms of the gingipains affect the extracellular proteolytic activity of RgpA, but not RgpB and Kgp. Glutamine statistics, mass spectrometry data and the mutagenesis results show that the N-terminal glutamine residues or their pyroglutamate cyclization products do not act as generic sorting signals.
Highlights
Bacteria of the Bacteroidetes phylum of gram-negatives live in very diverse habitats including human hosts (Thomas et al, 2011)
The starting point for this study was the observation that many secreted P. gingivalis proteins with predicted signal peptides had a glutamine (Q) residue immediately downstream. The generality of this observation was confirmed on a genome-wide basis using the batch version of SignalP
Starting from these sequences, and correcting for species duplicates, we identified 574 Bacteroidetes species containing animal-type and 507 Bacteroidetes species containing plant-type QC enzymes, but only 63 species containing both types of enzymes (E-value threshold 1E-4), compared to 1540 species in the duplication corrected proteome dataset
Summary
Bacteria of the Bacteroidetes phylum of gram-negatives live in very diverse habitats including human hosts (Thomas et al, 2011). Studies of the diversity of the healthy human microbiome in various tissues have shown that the Bacteroidetes colonize many human tissues. In the gut, they are abundant, and together with the Firmicutes, they comprise over 90% of the microbiome in Western populations (Human Microbiome Project Consortium, 2012; Johnson et al, 2017). Many Bacteroidetes species may cause significant clinical problems (Wexler, 2007). This is best illustrated by chronic periodontitis, the infection-driven inflammation of tooth-supporting tissues initiated and propagated by Porphyromonas gingivalis and Tannerella forsythia colonizing subgingival tooth surface (Holt and Ebersole, 2005; How et al, 2016). Protein secretion has been found to be essential for these species for interactions with the host, in part, but , because many identified virulence factors are secreted proteins (Green and Mecsas, 2016)
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