Commensal bacterium Clostridium paraputrificum J4 produces several extracellular chitinolytic enzymes including a 62 kDa chitinase Chit62J4 active toward 4-nitrophenyl N,N'-diacetyl-β-d-chitobioside (pNGG). We characterized the crude enzyme from bacterial culture fluid, recombinant enzyme rChit62J4, and its catalytic domain rChit62J4cat. This major chitinase, securing nutrition of the bacterium in the human intestinal tract when supplied with chitin, has a pH optimum of 5.5 and processes pNGG with Km = 0.24 mM and kcat = 30.0 s-1. Sequence comparison of the amino acid sequence of Chit62J4, determined during bacterial genome sequencing, characterizes the enzyme as a family 18 glycosyl hydrolase with a four-domain structure. The catalytic domain has the typical TIM barrel structure and the accessory domains-2x Fn3/Big3 and a carbohydrate binding module-that likely supports enzyme activity on chitin fibers. The catalytic domain is highly homologous to a single-domain chitinase of Bacillus cereus NCTU2. However, the catalytic profiles significantly differ between the two enzymes despite almost identical catalytic sites. The shift of pI and pH optimum of the commensal enzyme toward acidic values compared to the soil bacterium is the likely environmental adaptation that provides C. paraputrificum J4 a competitive advantage over other commensal bacteria.
- MeSH
- bakteriální proteiny genetika metabolismus MeSH
- chitin metabolismus MeSH
- chitinasy chemie genetika metabolismus MeSH
- Clostridium růst a vývoj izolace a purifikace metabolismus MeSH
- katalytická doména MeSH
- koncentrace vodíkových iontů MeSH
- lidé MeSH
- rekombinantní proteiny genetika metabolismus MeSH
- střevní mikroflóra MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Gram-stain-positive, catalase and oxidase-negative and short rod-shaped bacterium C10 with occasional branching was isolated under strictly anaerobic conditions from the rumen fluid of a red deer (Cervus elaphus) in the course of study attempting to uncover new xylanolytic and cellulolytic rumen bacteria inhabiting the digestive tract of wild ruminants in the Czech Republic. The anaerobic M10 medium containing bovine rumen fluid and carboxymethylcellulose as a defined source of organic carbon was used in the process of bacterial isolation. The 16S rRNA gene similarity revealed recently characterized new species Actinomyces succiniciruminis Am4T (GenBank accession number of the gene retrieved from the complete genome: LK995506) and Actinomyces glycerinitolerans G10T (GenBank accession number from the complete genome: NZFQTT01000017) as the closest relatives (99.7 and 99.6% gene pairwise identity, respectively), followed by the Actinomyces ruminicola DSM 27982T (97.2%, in all compared fragment of 41468 pb). Due to the taxonomic affinity of the examined strain to both species A. succiniciruminis and A. glycerinitolerans, its taxonomic status towards these species was evaluated using variable regions of rpsA (length of 519 bp) and rplB (597 bp) gene sequences amplified based on specific primers designed so as to be applicable in differentiation, classification, and phylogeny of Actinomyces species/strains. Comparative analyses using rpsA and rplB showed 98.5 and 97.9% similarities of C10 to A. succiniciruminis, respectively, and 97.5 and 97.6% similarities to A. glycerinitolerans, respectively. Thus, gene identities revealed that the evaluated isolate C10 (=DSM 100236 = LMG 28777) is a little more related to the species A. succiniciruminis isolated from the rumen of a Holstein-Friesian cow than A. glycerinitolerans. Phylogenetic analyses confirmed affinity of strain C10 to both recently characterized species. Unfortunately, they did not allow the bacterial strain to be classified into a particular species. Phenotypic characterization suggested similar conclusions. This brief contribution is aimed at classification and detailed phenotypic characterization of bacterial strain C10 isolated from the rumen of a wild red deer exhibiting, from the point of view of Actinomyces species, noteworthy cellulolytic and xylanolytic activities.
- MeSH
- Actinomyces klasifikace genetika izolace a purifikace metabolismus MeSH
- bachor mikrobiologie MeSH
- bakteriální geny genetika MeSH
- celulosa metabolismus MeSH
- DNA bakterií genetika MeSH
- fenotyp MeSH
- fylogeneze MeSH
- mastné kyseliny analýza MeSH
- peptidoglykan analýza MeSH
- RNA ribozomální 16S genetika MeSH
- vysoká zvěř mikrobiologie MeSH
- xylany metabolismus MeSH
- zastoupení bazí MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Publikační typ
- abstrakt z konference MeSH
- MeSH
- anaerobióza fyziologie MeSH
- anaerobní bakterie fyziologie MeSH
- mikrobiologie trendy MeSH
- Publikační typ
- úvodní články MeSH
- úvodníky MeSH
- Geografické názvy
- Rakousko MeSH
- MeSH
- anaerobióza MeSH
- mikrobiologie MeSH
- výzkum MeSH
- Publikační typ
- úvodní články MeSH
- Geografické názvy
- Slovenská republika MeSH
Antibacterial effect of chitooligosaccharides (COS) and low molar mass chitosans (LMWC) is considered as one of the most important characteristics of chitosan (CS) hydrolysates. Here, we show the in vitro effect of different COS, LMWC, and CS on representative anaerobic bacteria isolated from human colon as a possibility of targeting modification of colonic microflora composition by supplementation of dietary CS products by humans. Specific growth rate of seven selected nonpathogenic anaerobic bacterial strains (Clostridium paraputrificum, Clostridium beijerinckii, Roseburia intestinalis, Bacteroides vulgatus, Bacteriodes thetaiotaomicron, Faecalibacterium prausnitzii and Blautia coccoides) was determined in the presence of 0.25 and 0.5% COS (2, 3, and 6 kDa), 0.025 and 0.05% of LMWC (10 and 16 kDa), and 0.025 and 0.1% of CS in vitro. The growth rate decreased in all strains in the presence of COS and LMWC in higher concentrations in comparison to control incubations. A relatively higher resistance to CS hydrolyzates was detected in R. intestinalis and F. prausnitzii, and more susceptible were bacteria belonging to Bacteoides sp. and Clostridium sp. The antimicrobial activity, minimum inhibitory concentrations (MIC), and minimal bactericidal concentrations (MBC) were determined. The antimicrobial activity increased with the degree of polymerization (DP). MIC ranged from 0.25 to 4.5% in dependence on bacterial strain and DP of CS/LMWC. MBC also decreased with DP. The most effective antimicrobial action was detected in LMWC with 16 kDa and CS. Weak antimicrobial activity was found in COS with small molecules (2 and 3 kDa).
- MeSH
- antibakteriální látky chemie farmakologie MeSH
- Bacteria klasifikace účinky léků genetika izolace a purifikace MeSH
- chitosan chemie farmakologie MeSH
- kolon mikrobiologie MeSH
- lidé MeSH
- mikrobiální testy citlivosti MeSH
- molekulová hmotnost MeSH
- oligosacharidy chemie farmakologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
A strictly anaerobic mesophilic chitinolytic bacterial strain identified as Clostridium paraputrificum J4 was isolated from human feces. In response to various types of growth substrates, the bacterium produced an array of chitinolytic enzymes representing significant components of the J4 strain secretome. The excreted active proteins were characterized by estimating the enzymatic activities of endochitinase, exochitinase, and N-acetylglucosaminidase induced by cultivation in medium M-10 with colloidal chitin. The enzyme activities produced by J4 strain cultivated in medium M-10 with glucose were significantly lower. The spectrum of extracellularly excreted proteins was separated by SDS-PAGE. The chitinase variability was confirmed on zymograms of renatured SDS-PAGE. The enzymes were visualized under ultraviolet light by using 4-methylumbelliferyl derivatives of N-acetyl-β-D: -glucosaminide, N,N´-diacetyl-β-D: -chitobiose, or N,N´,N˝-triacetyl-β-D: -chitotriose for β-N-acetylglucosaminidase, chitobiosidase, or endochitinase activities, respectively. Protein components of the secretome were separated by 2D-PAGE analysis. The distinct protein bands were excised, isolated, and subsequently characterized by using MALDI-TOF/TOF tandem mass spectrometry. The final identification was performed according to sequence homology by database searching.
- MeSH
- 2D gelová elektroforéza MeSH
- acetylglukosaminidasa chemie genetika metabolismus MeSH
- bakteriální proteiny chemie genetika metabolismus MeSH
- chitinasy chemie genetika metabolismus MeSH
- Clostridium chemie enzymologie genetika izolace a purifikace MeSH
- extracelulární prostor chemie enzymologie genetika MeSH
- feces mikrobiologie MeSH
- hmotnostní spektrometrie MeSH
- lidé MeSH
- transport proteinů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The effect of the administration of chitosan (CS) and chitooligosaccharides (COS) on rat fecal microbiota was analyzed in this study. The profile of total bacterial population was monitored during 3 weeks of CS or COS application using denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene amplicons. Quantitative PCR was used for monitoring possible changes in the levels of total bacteria and the levels of individual bacterial groups: Bifidobacteria, Clostridium leptum, Enterobacteriaceae, Lactobacillus-Streptococcus-Enterobacter, and Bacteroides-Prevotella. The DGGE profiles revealed a high complexity and individuality of each tested subject, and variations in the composition of band pattern were observed. CS or COS per os administration changed the profile and structure of the microbial ecosystem of the gastrointestinal tract of healthy rats. COS have, in most cases, an opposite effect compared with CS; only the Bacteroides-Prevotella bacterial group and Enterobacteriaceae were influenced in the same way. The Bifidobacteria group was not influenced by the administration CS and COS.
- MeSH
- Bacteria klasifikace genetika izolace a purifikace MeSH
- chitosan aplikace a dávkování farmakologie MeSH
- feces mikrobiologie MeSH
- krysa rodu rattus MeSH
- metagenom účinky léků MeSH
- oligosacharidy aplikace a dávkování farmakologie MeSH
- potkani Wistar MeSH
- potravinářské přísady aplikace a dávkování farmakologie MeSH
- střeva mikrobiologie MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- mužské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The object of this study are chitinolytic enzymes produced by bacterium Clostridium paraputrificum J4 isolated from the gastrointestinal tract of a healthy human. In particular, we focus on the development of purification protocols, determination of properties of the enzymes and their activity profiles. The process of bacteria cultivation and isolation of chitinolytic complex of enzymes showing specific activities of endo-, exo-chitinase and N-acetyl-β-glucosaminidase was optimized. A range of various purification procedures were used such as ultrafiltration, precipitation, chromatographic separations (ion-exchange, size exclusion, chromatofocusing) in altered combinations. The optimal purification protocol comprises two or three steps. Individual samples were analyzed by SDS/PAGE electrophoresis and after renaturation their activity could be detected using zymograms. Mass spectroscopy peptide fragment analysis and MALDI analysis of the purest samples indicate presence of endochitinase B (molecular mass about 85 kDa) and of 60-kDa endo- and exochitinases.
- MeSH
- anaerobióza MeSH
- bakteriální proteiny izolace a purifikace metabolismus sekrece MeSH
- chitin metabolismus MeSH
- chitinasy izolace a purifikace metabolismus sekrece MeSH
- Clostridium enzymologie růst a vývoj MeSH
- gastrointestinální trakt mikrobiologie MeSH
- glykosidhydrolasy izolace a purifikace metabolismus sekrece MeSH
- hexosaminidasy izolace a purifikace metabolismus sekrece MeSH
- kultivační techniky metody MeSH
- lidé MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Membrane ultrafiltration (UF) was used in sample preparation of the culture fluids of the human intestinal bacterium Clostridium paraputrificum strain J4 containing seven extracellular chitinolytic isoenzymes (38-90 kDa). The subsequent filtration of the bacteria-free supernatants was carried out through Millipore membranes with cut-off 100 and 30 kDa for separation of undigested components of the culture medium and bacterial metabolites with molecular weight higher and lower than that of the target enzymes. The chitinolytic enzymes, which were the minor components in the culture fluids, were concentrated at UF as well. The aim of the research consisted in evaluation of the effect of component composition of bacteria-free supernatants and the chemical nature of membrane active layer on partial fractionation of the chitinolytic enzymes, their recovery in retentates and purification degree. On the basis of the obtained experimental results, the sample preparation procedure of the culture fluids of C. paraputrificum J4 was established to be used further in chromatographic separations of the chitinolytic enzymes.
- MeSH
- bakteriální proteiny izolace a purifikace metabolismus MeSH
- chitinasy izolace a purifikace metabolismus MeSH
- Clostridium enzymologie růst a vývoj MeSH
- elektroforéza v polyakrylamidovém gelu MeSH
- kultivační média MeSH
- lidé MeSH
- membrány umělé MeSH
- průmyslová mikrobiologie MeSH
- střeva mikrobiologie MeSH
- ultrafiltrace metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
