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  1. Article ; Online: Mapping the substrate-binding subsite specificity of a Porphyromonas gingivalis Tpr peptidase.

    Staniec, Dominika / Rut, Wioletta / Drag, Marcin / Burmistrz, Michal / Kitching, Michael / Potempa, Jan

    Acta biochimica Polonica

    2023  Volume 70, Issue 4, Page(s) 963–968

    Abstract: Calcium-dependent peptidases of the calpain family are widespread in eukaryotes but uncommon in prokaryotes. A few bacterial calpain homologs have been discovered but none of them have been characterized in detail. Here we present an in-depth substrate ... ...

    Abstract Calcium-dependent peptidases of the calpain family are widespread in eukaryotes but uncommon in prokaryotes. A few bacterial calpain homologs have been discovered but none of them have been characterized in detail. Here we present an in-depth substrate specificity analysis of the bacterial calpain-like peptidase Tpr from Porphyromonas gingivalis. Using the positional scanning hybrid combinatorial substrate library method, we found that the specificity of Tpr peptidase differs substantially from the papain family of cysteine proteases, showing a strong preference for proline residues at positions P2 and P3. Such a degree of specificity indicates that this P. gingivalis cell-surface peptidase has a more sophisticated role than indiscriminate protein degradation to generate peptide nutrients, and may fulfil virulence-related functions such as immune evasion.
    MeSH term(s) Porphyromonas gingivalis/genetics ; Porphyromonas gingivalis/metabolism ; Peptide Hydrolases/metabolism ; Calpain/genetics ; Calpain/metabolism ; Substrate Specificity ; Endopeptidases/metabolism
    Chemical Substances Peptide Hydrolases (EC 3.4.-) ; Calpain (EC 3.4.22.-) ; Endopeptidases (EC 3.4.-)
    Language English
    Publishing date 2023-12-08
    Publishing country Poland
    Document type Journal Article
    ZDB-ID 595762-x
    ISSN 1734-154X ; 0001-527X
    ISSN (online) 1734-154X
    ISSN 0001-527X
    DOI 10.18388/abp.2020_6904
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs in the Porphyromonas gingivalis CRISPR-Cas I-C System.

    Burmistrz, Michal / Rodriguez Martinez, Jose Ignacio / Krochmal, Daniel / Staniec, Dominika / Pyrc, Krzysztof

    Journal of bacteriology

    2017  Volume 199, Issue 23

    Abstract: The CRISPR-Cas (clustered regularly interspaced short palindromic repeat-CRISPR-associated protein) system is unique to prokaryotes and provides the majority of bacteria and archaea with immunity against nucleic acids of foreign origin. CRISPR RNAs ( ... ...

    Abstract The CRISPR-Cas (clustered regularly interspaced short palindromic repeat-CRISPR-associated protein) system is unique to prokaryotes and provides the majority of bacteria and archaea with immunity against nucleic acids of foreign origin. CRISPR RNAs (crRNAs) are the key element of this system, since they are responsible for its selectivity and effectiveness. Typical crRNAs consist of a spacer sequence flanked with 5' and 3' handles originating from repeat sequences that are important for recognition of these small RNAs by the Cas machinery. In this investigation, we studied the type I-C CRISPR-Cas system in
    MeSH term(s) CRISPR-Associated Proteins/genetics ; CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Gene Transfer, Horizontal/genetics ; Porphyromonas gingivalis/genetics ; RNA/genetics
    Chemical Substances CRISPR-Associated Proteins ; RNA (63231-63-0)
    Language English
    Publishing date 2017-10-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.00275-17
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Functional Analysis of Porphyromonas gingivalis W83 CRISPR-Cas Systems.

    Burmistrz, Michał / Dudek, Bartosz / Staniec, Dominika / Rodriguez Martinez, Jose Ignacio / Bochtler, Matthias / Potempa, Jan / Pyrc, Krzysztof

    Journal of bacteriology

    2015  Volume 197, Issue 16, Page(s) 2631–2641

    Abstract: Unlabelled: The CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system provides prokaryotic cells with an adaptive and heritable immune response to foreign genetic elements, such as viruses, plasmids, and ... ...

    Abstract Unlabelled: The CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system provides prokaryotic cells with an adaptive and heritable immune response to foreign genetic elements, such as viruses, plasmids, and transposons. It is present in the majority of Archaea and almost half of species of Bacteria. Porphyromonas gingivalis is an important human pathogen that has been proven to be an etiological agent of periodontitis and has been linked to systemic conditions, such as rheumatoid arthritis and cardiovascular disease. At least 95% of clinical strains of P. gingivalis carry CRISPR arrays, suggesting that these arrays play an important function in vivo. Here we show that all four CRISPR arrays present in the P. gingivalis W83 genome are transcribed. For one of the arrays, we demonstrate in vivo activity against double-stranded DNA constructs containing protospacer sequences accompanied at the 3' end by an NGG protospacer-adjacent motif (PAM). Most of the 44 spacers present in the genome of P. gingivalis W83 share no significant similarity with any known sequences, although 4 spacers are similar to sequences from bacteria found in the oral cavity and the gastrointestinal tract. Four spacers match genomic sequences of the host; however, none of these is flanked at its 3' terminus by the appropriate PAM element.
    Importance: The CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system is a unique system that provides prokaryotic cells with an adaptive and heritable immunity. In this report, we show that the CRISPR-Cas system of P. gingivalis, an important human pathogen associated with periodontitis and possibly also other conditions, such as rheumatoid arthritis and cardiovascular disease, is active and provides protection from foreign genetic elements. Importantly, the data presented here may be useful for better understanding the communication between cells in larger bacterial communities and, consequently, the process of disease development and progression.
    MeSH term(s) Amino Acid Sequence ; CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Culture Media/chemistry ; DNA/genetics ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Genetic Loci ; Genome, Bacterial ; Molecular Sequence Data ; Plasmids/genetics ; Porphyromonas gingivalis/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Transcriptional Activation
    Chemical Substances Culture Media ; DNA Transposable Elements ; DNA, Bacterial ; DNA (9007-49-2)
    Language English
    Publishing date 2015-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.00261-15
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Calcium Regulates the Activity and Structural Stability of Tpr, a Bacterial Calpain-like Peptidase.

    Staniec, Dominika / Ksiazek, Miroslaw / Thøgersen, Ida B / Enghild, Jan J / Sroka, Aneta / Bryzek, Danuta / Bogyo, Matthew / Abrahamson, Magnus / Potempa, Jan

    The Journal of biological chemistry

    2015  Volume 290, Issue 45, Page(s) 27248–27260

    Abstract: Porphyromonas gingivalis is a peptide-fermenting asaccharolytic periodontal pathogen. Its genome contains several genes encoding cysteine peptidases other than gingipains. One of these genes (PG1055) encodes a protein called Tpr (thiol protease) that has ...

    Abstract Porphyromonas gingivalis is a peptide-fermenting asaccharolytic periodontal pathogen. Its genome contains several genes encoding cysteine peptidases other than gingipains. One of these genes (PG1055) encodes a protein called Tpr (thiol protease) that has sequence similarity to cysteine peptidases of the papain and calpain families. In this study we biochemically characterize Tpr. We found that the 55-kDa Tpr inactive zymogen proteolytically processes itself into active forms of 48, 37, and 33 kDa via sequential truncations at the N terminus. These processed molecular forms of Tpr are associated with the bacterial outer membrane where they are likely responsible for the generation of metabolic peptides required for survival of the pathogen. Both autoprocessing and activity were dependent on calcium concentrations >1 mm, consistent with the protein's activity within the intestinal and inflammatory milieus. Calcium also stabilized the Tpr structure and rendered the protein fully resistant to proteolytic degradation by gingipains. Together, our findings suggest that Tpr is an example of a bacterial calpain, a calcium-responsive peptidase that may generate substrates required for the peptide-fermenting metabolism of P. gingivalis. Aside from nutrient generation, Tpr may also be involved in evasion of host immune response through degradation of the antimicrobial peptide LL-37 and complement proteins C3, C4, and C5. Taken together, these results indicate that Tpr likely represents an important pathogenesis factor for P. gingivalis.
    MeSH term(s) Amino Acid Sequence ; Animals ; Antimicrobial Cationic Peptides/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Calcium/metabolism ; Calpain/chemistry ; Calpain/genetics ; Calpain/metabolism ; Caseins/metabolism ; Catalytic Domain/genetics ; Cattle ; Endopeptidases/chemistry ; Endopeptidases/genetics ; Endopeptidases/metabolism ; Enzyme Stability ; Fibrinogen/metabolism ; Fibronectins/metabolism ; Genes, Bacterial ; Humans ; Kinetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Porphyromonas gingivalis/enzymology ; Porphyromonas gingivalis/genetics ; Porphyromonas gingivalis/pathogenicity ; Proteolysis ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Substrate Specificity
    Chemical Substances Antimicrobial Cationic Peptides ; Bacterial Proteins ; Caseins ; Fibronectins ; Recombinant Proteins ; ropocamptide (3DD771JO2H) ; Fibrinogen (9001-32-5) ; Endopeptidases (EC 3.4.-) ; Calpain (EC 3.4.22.-) ; tpr protease (EC 3.4.99.-) ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2015-09-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M115.648782
    Database MEDical Literature Analysis and Retrieval System OnLINE

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