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Nakamura A, Honma N, Tanaka Y, Suzuki Y, Shida Y, Tsuda Y, Hidaka K, Ogasawara W. 7-Aminocoumarin-4-acetic Acid as a Fluorescent Probe for Detecting Bacterial Dipeptidyl Peptidase Activities in Water-in-Oil Droplets and in Bulk. Anal Chem 2021; 94:2416-2424. [PMID: 34963280 PMCID: PMC8886566 DOI: 10.1021/acs.analchem.1c04108] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Droplet-based
microfluidic systems are a powerful tool for biological
assays with high throughput. Water-in-oil droplets (WODLs) are typically
used in droplet-based microfluidic systems to culture microorganisms
and perform enzyme assays. However, because of the oil surrounding
the nanoliter and picoliter volumes of WODLs, availability of suitable
substrates is limited. For instance, although 7-amino-4-methylcoumarin
(AMC) is commonly used as a fluorescent probe of the substrate to
detect peptidase activity, AMC leaks from WODLs to the oil phase due
to its high hydrophobicity. Thus, AMC substrates cannot be used in
droplet-based microfluidic systems with WODLs. In this study, we developed
a peptidase substrate consisting of a dipeptide and 7-aminocoumarin-4-acetic
acid (ACA), an AMC-derived fluorogenic compound. ACA was retained
in the WODL for more than 7 days, and the dipeptidyl ACA substrate
detected dipeptidyl peptidase (DPP) activity in the WODL. Compared
to AMC substrates, the substrate specificity constants of DPPs for
ACA substrates increased up to 4.7-fold. Fluorescence-activated droplet
sorting made high-throughput screening of microorganisms based on
DPP activity using the dipeptidyl ACA substrate possible. Since ACA
could be applied to various substrates as a fluorescent probe, detectable
microbial enzyme activities for droplet-based microfluidic systems
can be largely expanded.
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Affiliation(s)
- Akihiro Nakamura
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Nobuyuki Honma
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yuma Tanaka
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yoshiyuki Suzuki
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yuko Tsuda
- Faculty of Pharmaceutical Sciences, Cooperative Research Center of Life Sciences, Kobe Gakuin University, 1-1-3 Minatojima, Chuo-ku, Kobe, Hyogo 650-8586, Japan
| | - Koushi Hidaka
- Graduate School of Health Sciences, Kobe University, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo 654-0142, Japan
| | - Wataru Ogasawara
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.,Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7. Sci Rep 2021; 11:7929. [PMID: 33846449 PMCID: PMC8041751 DOI: 10.1038/s41598-021-86965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The emergence of drug-resistant bacteria has become a major problem worldwide. Bacterial dipeptidyl peptidases 7 and 11 (DPP7s and DPP11s), belonging to the family-S46 peptidases, are important enzymes for bacterial growth and are not present in mammals. Therefore, specific inhibitors for these peptidases are promising as potential antibiotics. While the molecular mechanisms underlining strict specificity at the S1 subsite of S46 peptidases have been well studied, those of relatively broad preference at the S2 subsite of these peptidases are unknown. In this study, we performed structural and biochemical analyses on DPP7 from Stenotrophomonas maltophilia (SmDPP7). SmDPP7 showed preference for the accommodation of hydrophobic amino acids at the S2 subsite in general, but as an exception, also for asparagine, a hydrophilic amino acid. Structural analyses of SmDPP7 revealed that this exceptional preference to asparagine is caused by a hydrogen bonding network at the bottom of the S2 subsite. The residues in the S2 subsite are well conserved among S46 peptidases as compared with those in the S1 subsite. We expect that our findings will contribute toward the development of a universal inhibitor of S46 peptidases.
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Nemoto TK, Ohara Nemoto Y. Dipeptidyl-peptidases: Key enzymes producing entry forms of extracellular proteins in asaccharolytic periodontopathic bacterium Porphyromonas gingivalis. Mol Oral Microbiol 2020; 36:145-156. [PMID: 33006264 PMCID: PMC8048996 DOI: 10.1111/omi.12317] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/17/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023]
Abstract
Porphyromonas gingivalis, a pathogen of chronic periodontitis, is an asaccharolytic microorganism that solely utilizes nutritional amino acids as its energy source and cellular constituents. The bacterium is considered to incorporate proteinaceous nutrients mainly as dipeptides, thus exopeptidases that produce dipeptides from polypeptides are critical for survival and proliferation. We present here an overview of dipeptide production by P. gingivalis mediated by dipeptidyl-peptidases (DPPs), e.g., DPP4, DPP5, DPP7, and DPP11, serine exopeptidases localized in periplasm, which release dipeptides from the N-terminus of polypeptides. Additionally, two other exopeptidases, acylpeptidyl-oligopeptidase (AOP) and prolyl tripeptidyl-peptidase A (PTP-A), which liberate N-terminal acylated di-/tri-peptides and tripeptides with Pro at the third position, respectively, provide polypeptides in an acceptable form for DPPs. Hence, a large fraction of dipeptides is produced from nutritional polypeptides by DPPs with differential specificities in combination with AOP and PTP-A. The resultant dipeptides are then incorporated across the inner membrane mainly via a proton-dependent oligopeptide transporter (POT), a member of the major facilitator superfamily. Recent studies also indicate that DPP4 and DPP7 directly link between periodontal and systemic diseases, such as type 2 diabetes mellitus and coagulation abnormality, respectively. Therefore, these dipeptide-producing and incorporation molecules are considered to be potent targets for prevention and treatment of periodontal and related systemic diseases.
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Affiliation(s)
- Takayuki K Nemoto
- Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuko Ohara Nemoto
- Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Hansen NW, Sams A. The Microbiotic Highway to Health-New Perspective on Food Structure, Gut Microbiota, and Host Inflammation. Nutrients 2018; 10:E1590. [PMID: 30380701 PMCID: PMC6267475 DOI: 10.3390/nu10111590] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/13/2018] [Accepted: 10/23/2018] [Indexed: 12/14/2022] Open
Abstract
This review provides evidence that not only the content of nutrients but indeed the structural organization of nutrients is a major determinant of human health. The gut microbiota provides nutrients for the host by digesting food structures otherwise indigestible by human enzymes, thereby simultaneously harvesting energy and delivering nutrients and metabolites for the nutritional and biological benefit of the host. Microbiota-derived nutrients, metabolites, and antigens promote the development and function of the host immune system both directly by activating cells of the adaptive and innate immune system and indirectly by sustaining release of monosaccharides, stimulating intestinal receptors and secreting gut hormones. Multiple indirect microbiota-dependent biological responses contribute to glucose homeostasis, which prevents hyperglycemia-induced inflammatory conditions. The composition and function of the gut microbiota vary between individuals and whereas dietary habits influence the gut microbiota, the gut microbiota influences both the nutritional and biological homeostasis of the host. A healthy gut microbiota requires the presence of beneficial microbiotic species as well as vital food structures to ensure appropriate feeding of the microbiota. This review focuses on the impact of plant-based food structures, the "fiber-encapsulated nutrient formulation", and on the direct and indirect mechanisms by which the gut microbiota participate in host immune function.
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Affiliation(s)
- Nina Wærling Hansen
- Molecular Endocrinology Unit (KMEB), Department of Endocrinology, Institute of Clinical Research, University of Southern Denmark, DK-5000 Odense, Denmark.
| | - Anette Sams
- Department of Clinical Experimental Research, Glostrup Research Institute, Copenhagen University Hospital, Nordstjernevej 42, DK-2600 Glostrup, Denmark.
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