A Gram-stain-positive, rod-shaped, aerobic, motile bacterium, J379T, was isolated from radioactive water spring C1, located in a former silver-uranium mine in the Czech Republic. This slow-growing strain exhibited optimal growth at 24-28 °C on solid media with <1 % salt concentration and alkaline pH 8-10. The only respiratory quinone found in strain J379T was MK-7(H4). C18 : 1 ω9c (60.9 %), C18 : 0 (9.4 %), C16 : 0 and alcohol-C18 : 0 (both 6.2 %) were found to be the major fatty acids. The peptidoglycan contained directly cross-linked meso-diaminopimelic acid. Phylogenetic reconstruction based on the 16S rRNA gene sequences and the core-genome analysis revealed that strain J379T forms a separate phylogenetic lineage within the recently amended order Solirubrobacterales. A comparison of the 16S rRNA gene sequences between strain J379T and other members of the order Solirubrobacterales showed <96 % similarity. This analysis revealed that the closest type strains were Parviterribacter kavangonensis D16/0 /H6T (95.2 %), Capillimicrobium parvum 0166_1T (94.9 %) and Conexibacter arvalis KV-962T (94.5 %). Whole-genome analysis showed that the closest type strain was Baekduia soli BR7-21T with an average nucleotide identity of 78 %, average amino acid identity of 63.2 % and percentage of conserved proteins of 48.2 %. The G+C content of the J379T genomic DNA was 71.7 mol%. Based on the phylogenetic and phylogenomic data, as well as its physiological characteristics, strain J379T is proposed to represent a type strain (DSM 113746T=CCM 9300T) of Svornostia abyssi gen. nov. sp. nov. within the family Baekduiaceae.
- Klíčová slova
- Svornostia abyssi, mineral springs, novel bacterial taxa, slow-growing bacterium,
- MeSH
- DNA bakterií * genetika MeSH
- fylogeneze * MeSH
- hornictví * MeSH
- kyselina diaminopimelová analýza MeSH
- mastné kyseliny * chemie analýza MeSH
- mikrobiologie vody MeSH
- peptidoglykan MeSH
- RNA ribozomální 16S * genetika MeSH
- sekvenční analýza DNA * MeSH
- stříbro MeSH
- techniky typizace bakterií * MeSH
- vitamin K 2 analogy a deriváty analýza MeSH
- zastoupení bazí * MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
- Názvy látek
- DNA bakterií * MeSH
- kyselina diaminopimelová MeSH
- mastné kyseliny * MeSH
- menaquinone 7 MeSH Prohlížeč
- peptidoglykan MeSH
- RNA ribozomální 16S * MeSH
- stříbro MeSH
- vitamin K 2 MeSH
A novel actinobacterial strain, designated 15TR583T, was isolated from a waterlogged acidic soil collected near the town of Trebon, Czech Republic, and was subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that the organism forms an individual line of descent related to the order Streptosporangiales, class Actinomycetia. The strain shared highest 16S rRNA gene sequence similarity, yet of only 92.8%, with Actinocorallia aurea IFO 14752T. The strain grew in white colonies of aerobic, Gram-stain-positive, unbranching substrate mycelium bearing single spores at hyphae tips. The major fatty acids (>10%) were iso-C16 : 0, C16 : 0, iso-C17 : 1ω9 and 10-methyl-C17 : 0. The fatty acid pattern differed from all patterns currently described for actinobacterial genera. The organism contained as major menaquinones MK9(H6) and MK9(H8), which differentiated it from other actinobacterial families. Polar lipids were composed of six unidentified glycolipids, an unidentified phosphoglycolipid, two unidentified phospholipids and two unidentified aminolipids. Whole-cell sugars contained galactose, xylose and arabinose as major components. The peptidoglycan type was A1γ meso-diaminopimelic acid. The genomic DNA G+C content was 69.7 mol%. The distinct phylogenetic position and unusual combination of chemotaxonomic characteristics justify the proposal of Trebonia gen. nov., with the type species Trebonia kvetii sp. nov. (type strain 15TR583T=CCM 8942T=DSM 109105T), within Treboniaceae fam. nov.
- Klíčová slova
- acidic soil, acidophilic, actinobacteria,
- MeSH
- Actinobacteria klasifikace izolace a purifikace MeSH
- buněčná stěna chemie MeSH
- DNA bakterií genetika MeSH
- fosfolipidy chemie MeSH
- fylogeneze * MeSH
- glykolipidy chemie MeSH
- kyselina diaminopimelová chemie MeSH
- mastné kyseliny chemie MeSH
- peptidoglykan chemie MeSH
- půdní mikrobiologie * MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- techniky typizace bakterií MeSH
- vitamin K 2 analogy a deriváty chemie MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
- Názvy látek
- DNA bakterií MeSH
- fosfolipidy MeSH
- glykolipidy MeSH
- kyselina diaminopimelová MeSH
- mastné kyseliny MeSH
- menaquinone 9 MeSH Prohlížeč
- peptidoglykan MeSH
- RNA ribozomální 16S MeSH
- vitamin K 2 MeSH
Strain CCM 4446T, with notable biodegradation capabilities, was investigated in this study in order to elucidate its taxonomic position. Chemotaxonomic analyses of quinones, polar lipids, mycolic acids, polyamines and the diamino acid of the cell-wall peptidoglycan corresponded with characteristics of the genus Rhodococcus. Phylogenetic analysis, based on the 16S rRNA gene sequence, assigned strain CCM 4446T to the genus Rhodococcus and placed it in the Rhodococcus erythropolis 16S rRNA gene clade. Further analysis of catA and gyrB gene sequences, automated ribotyping with EcoRI restriction endonuclease, whole-cell protein profiling, DNA-DNA hybridization and extensive biotyping enabled differentiation of strain CCM 4446T from all phylogenetically closely related species, i.e., Rhodococcus baikonurensis, Rhodococcus qingshengii, Rhodococcus erythropolis and Rhodococcus globerulus. The results obtained show that the strain investigated represents a novel species within the genus Rhodococcus, for which the name Rhodococcus degradans sp. nov., is proposed. The type strain is CCM 4446T ( = LMG 28633T).
- MeSH
- bakteriální geny MeSH
- DNA bakterií genetika MeSH
- fosfolipidy chemie MeSH
- fylogeneze * MeSH
- hybridizace nukleových kyselin MeSH
- kyselina diaminopimelová chemie MeSH
- kyseliny mykolové chemie MeSH
- mastné kyseliny chemie MeSH
- molekulární sekvence - údaje MeSH
- peptidoglykan chemie MeSH
- polyaminy chemie MeSH
- půdní mikrobiologie * MeSH
- Rhodococcus klasifikace genetika izolace a purifikace MeSH
- ribotypizace MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- techniky typizace bakterií MeSH
- vitamin K 2 chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Švýcarsko MeSH
- Názvy látek
- DNA bakterií MeSH
- fosfolipidy MeSH
- kyselina diaminopimelová MeSH
- kyseliny mykolové MeSH
- mastné kyseliny MeSH
- peptidoglykan MeSH
- polyaminy MeSH
- RNA ribozomální 16S MeSH
- vitamin K 2 MeSH
Thirteen mono-N-acyl derivatives of 2,6-diaminopimelic acid (DAP)-new potential inhibitors of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE; EC 3.5.1.18)-were analyzed and characterized by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopies and two capillary electromigration methods: capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC). Structural features of DAP derivatives were characterized by IR and NMR spectroscopies, whereas CZE and MEKC were applied to evaluate their purity and to investigate their electromigration properties. Effective electrophoretic mobilities of these compounds were determined by CZE in acidic and alkaline background electrolytes (BGEs) and by MEKC in acidic and alkaline BGEs containing a pseudostationary phase of anionic detergent sodium dodecyl sulfate (SDS) or cationic detergent cetyltrimethylammonium bromide (CTAB). The best separation of DAP derivatives, including diastereomers of some of them, was achieved by MEKC in an acidic BGE (500 mM acetic acid [pH 2.54] and 60mM SDS). All DAP derivatives were examined for their ability to inhibit catalytic activity of DapE from Haemophilus influenzae (HiDapE) and ArgE from Escherichia coli (EcArgE). None of these DAP derivatives worked as an effective inhibitor of HiDapE, but one derivative-N-fumaryl, Me-ester-DAP-was found to be a moderate inhibitor of EcArgE, thereby providing a promising lead structure for further studies on ArgE inhibitors.
- Klíčová slova
- 2,6-Diaminopimelic acid derivatives, Capillary zone electrophoresis, Enzyme inhibition, IR spectroscopy, Micellar electrokinetic chromatography, NMR spectroscopy,
- MeSH
- amidohydrolasy antagonisté a inhibitory MeSH
- elektroforéza kapilární metody MeSH
- Escherichia coli enzymologie MeSH
- Haemophilus influenzae enzymologie MeSH
- inhibitory enzymů chemie farmakologie MeSH
- kyselina diaminopimelová chemie MeSH
- magnetická rezonanční spektroskopie metody MeSH
- spektrofotometrie infračervená metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Názvy látek
- amidohydrolasy MeSH
- inhibitory enzymů MeSH
- kyselina diaminopimelová MeSH
- N-acetylornithine deacetylase MeSH Prohlížeč
- succinyldiaminopimelate desuccinylase MeSH Prohlížeč
The search for potential inhibitors that target so far unexplored bacterial enzyme mono-N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) has stimulated a development of methodology for quick and efficient preparation of mono-N-acylated 2,6-diaminopimelic acid (DAP) derivatives bearing the different carboxyl groups or lipophilic moieties on their amino group.
- MeSH
- acylace MeSH
- biomimetické materiály chemická syntéza chemie MeSH
- hmotnostní spektrometrie s elektrosprejovou ionizací MeSH
- kyselina diaminopimelová analogy a deriváty chemická syntéza chemie MeSH
- metabolické sítě a dráhy MeSH
- molekulární modely MeSH
- sukcináty chemická syntéza chemie MeSH
- sukcinyldiaminopimeláttransaminasa antagonisté a inhibitory metabolismus MeSH
- vysokoúčinná kapalinová chromatografie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- kyselina diaminopimelová MeSH
- sukcináty MeSH
- sukcinyldiaminopimeláttransaminasa MeSH
The method of the use of the HD 1200-E automatic amino acid analyzer for the separation of amino acids was modified for the determination of 2-6-diaminopimelic acid (DAPA) as a bacterial marker, besides the other amino acids in the acid hydrolyzates of samples of bacteria isolated from the rumen of sheep. The reproducibility of the determination of DAPA in a standard amino acid mixture found in the tests corresponded with the reproducibility of the determination of the other amino acids as indicated by the manufacturer of the apparatus. The lower limit of DAPA determination sensitivity is between 2 and 5 nmol. In samples of bacteria isolated from rumen wall, from feed particles of rumen contents and from rumen fluid, different contents of nitrogen and DAPA were obtained; this is ascribed to the different proportions of bacterial species in the bacterial populations having different functions.
- MeSH
- aminokyseliny diaminové analýza MeSH
- bachor mikrobiologie MeSH
- Bacteria analýza MeSH
- kyselina diaminopimelová analýza MeSH
- metody MeSH
- ovce mikrobiologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- anglický abstrakt MeSH
- časopisecké články MeSH
- Názvy látek
- aminokyseliny diaminové MeSH
- kyselina diaminopimelová MeSH
The strain designated Actinoplanes sp. 220 differed in its characteristics from other strains of the genus Actinoplanes listed in Bergey's Manual (1974). The strain belongs to psychrophilic culture growing within the range of 0-30 degrees C. The optimal temperature for growth on yeast--malt agar is 10-23 degrees C. Cultures transferred at 23 and 28 degrees C differed in morphological and physiological properties, enzyme activity and pigmentation in standard media. Submerged culture transferred at 28 degrees C inhibited growth of Bacillus subtilis ATCC 6633 and ATCC 9945. LL-2,6-Diaminopimelic acid was chromatographically detected in the submerged mycelium of this culture. This compound was not found in the mycelium of the original culture transferred at 23 degrees C. The cultures did not substantially differ in the composition of other amino acids contained in larger quantities in the mycelium.
- MeSH
- Bacillus cereus růst a vývoj metabolismus ultrastruktura MeSH
- buněčná stěna metabolismus ultrastruktura MeSH
- kultivační média MeSH
- kyselina diaminopimelová metabolismus MeSH
- spory bakteriální růst a vývoj metabolismus ultrastruktura MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- kultivační média MeSH
- kyselina diaminopimelová MeSH
Defects in the formation of the septum and gradually autolysis of cells occur when the dap-dependent mutant of Escherichia coli is grown in a medium with 4-hydroxy-diaminopimelic acid. When the culture grown in the presence of the labelled analogue is supplemented with the non-radioactive diaminopimelic acid a portion of the TCA-soluble radioactivity is released from the cells during 20 min after the addition of diaminopimelic acid. During this time interval the elongated forms formed in the presence of the analogue divide, however, only on the condition that the above forms are not irreversibly damaged. The increased concentration of the analogue in the medium substantially suppresses the irregularities in the development of the septum as well as the degradation of analogue containing cell wall. However, the growth rate in the presence of the analogue is always slightly lower than that in the presence of diaminopimelic acid. The cell wall pulse-labelled with diaminopimelic acid or its analogue for a time interval shorter than 1/4 of the generation time exhibits the same or only slightly higher rate of diaminopimelic acid is probably utilized less effectively for the synthesis of murein than diaminopimelic acid. However, its incorporation into the wall does not result in pronounced damage of the cell.
- MeSH
- buněčná stěna metabolismus MeSH
- buněčné dělení MeSH
- Escherichia coli růst a vývoj metabolismus MeSH
- hydroxykyseliny metabolismus MeSH
- kyselina diaminopimelová analogy a deriváty metabolismus MeSH
- kyseliny pimelové metabolismus MeSH
- mutace MeSH
- peptidoglykan biosyntéza metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- hydroxykyseliny MeSH
- kyselina diaminopimelová MeSH
- kyseliny pimelové MeSH
- peptidoglykan MeSH
- MeSH
- Bacillus megaterium cytologie růst a vývoj metabolismus MeSH
- bakteriolýza MeSH
- buněčná membrána MeSH
- buněčná stěna účinky léků metabolismus MeSH
- kyseliny pimelové metabolismus MeSH
- muramidasa farmakologie MeSH
- peptidoglykan metabolismus MeSH
- radioizotopy uhlíku MeSH
- teplota MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- kyseliny pimelové MeSH
- muramidasa MeSH
- peptidoglykan MeSH
- radioizotopy uhlíku MeSH
