Identification of a new subtype of dipeptidyl peptidase 11 and a third group of the S46-family members specifically present in the genus Bacteroides

Abstract

Peptidase family S46 consists of two types of dipeptidyl-peptidases (DPPs), DPP7 and DPP11, which liberate dipeptides from the N-termini of polypeptides along with the penultimate hydrophobic and acidic residues, respectively. Their specificities are primarily defined by a single amino acid residue, Gly in DPP7 and Arg in DPP11 (numbering for Porphyromonas gingivalis DPP11). Bacterial species in the phyla Proteobacteria and Bacteroidetes generally possess one gene for each, while Bacteroides species exceptionally possess three genes, one gene as DPP7 and two genes as DPP11, annotated based on the full-length similarities. In the present study, we aimed to characterize the above-mentioned Bacteroides S46 DPPs. A recombinant protein of the putative DPP11 gene BF9343_2924 from Bacteroides fragilis harboring Gly exhibited DPP7 activity by hydrolyzing Leu-Leu-4-methylcoumaryl-7-amide (MCA). Another gene, BF9343_2925, as well as the Bacteroides vulgatus gene (BVU_2252) with Arg was confirmed to encode DPP11. These results demonstrated that classification of S46 peptidase is enforceable by the S1 essential residues. Bacteroides DPP11 showed a decreased level of activity towards the substrates, especially with P1-position Glu. Findings of 3D structural modeling indicated three potential amino acid substitutions responsible for the reduction, one of which, Asn650Thr substitution, actually recovered the hydrolyzing activity of Leu-Glu-MCA. On the other hand, the gene currently annotated as DPP7 carrying Gly from B. fragilis (BF9343_0130) and Bacteroides ovatus (Bovatus_03382) did not hydrolyze any of the examined substrates. The existence of a phylogenic branch of these putative Bacteroides DPP7 genes classified by the C-terminal conserved region (Ser-Leu) strongly suggests that Bacteroides species expresses a DPP with an unknown property. In conclusion, the genus Bacteroides exceptionally expresses three S46-family members; authentic DPP7, a new subtype of DPP11 with substantially reduced specificity for Glu, and a third group of S46 family members.

7-Aminocoumarin-4-acetic Acid as a Fluorescent Probe for Detecting Bacterial Dipeptidyl Peptidase Activities in Water-in-Oil Droplets and in Bulk

“…Similar to the FADS (Met–Leu–ACA) sample, some species classified as Aeromonadaceae, Oxalobacteraceae, Weeksellaceae, or Pseudomonadaceae belong to the Proteobacteria or Bacteroidetes phylum and possess the S46 peptidases. 24 , 40 , 41 Therefore, these results support that the screening of microorganisms based on DPP activity using the dipeptidyl ACA substrates succeeded in enriching the abundance of microorganisms possibly through bacterial DPP7 or DPP11.…”

“…Some species classified as Xanthomonadaceae, Moraxellaceae, Oxalobacteraceae, or Weeksellaceae, which belong to Proteobacteria or Bacteroidetes, possess bacterial DPP7 and DPP11. 24 , 40 , 41 For the FADS (Leu–Asp–ACA) sample, the abundance ratio of Aeromonadaceae (denovo1771) increased the most, by 55.1-fold. The abundance ratios of Weeksellaceae (denovo1186), Oxalobacteraceae (denovo1645), and Pseudomonadaceae (denovo3742) increased 48.7-fold, 31.1-fold, and 23.3-fold, respectively, compared to the tofu factory waste fluid sample.…”

Dipeptidyl‐peptidases: Key enzymes producing entry forms of extracellular proteins in asaccharolytic periodontopathic bacterium Porphyromonas gingivalis

“…The acidic P1‐position residue is recognized by Arg673 in P. gingivalis DPP11. Biochemical studies have revealed that there are three subtypes of DPP11; (a) Porphyromonas‐ type DPP11, which is Asp‐preferential, (b) Bacteroides‐ type DPP11, which shows a high preference for Asp and scarcely accepts Glu, and (c) Shewanella‐ type DPP11, in which S1 Ser673 instead of Arg673, primarily exhibits higher preference for Glu (Nemoto et al., 2017).…”

The Microbiotic Highway to Health—New Perspective on Food Structure, Gut Microbiota, and Host Inflammation

“…Some bacterial genera e.g., Bacteroides [ 92 ] and Lactobacillus [ 93 ] secrete both peptidases and glycosidases and the more distal fiber-fermenting species Bacteroides thetaiotaomicron also express dipeptidylpeptidases (DPPs) [ 94 , 95 ]. Interestingly, the DPP4 antagonist vildagliptin, used for the treatment of T2D, induces a higher relative abundance of Bacteroidetes , a lower abundance of Firmicutes , and thus a reduced ratio of Firmicutes/Bacteroidetes in rats [ 96 ].…”