Strain identifier

BacDive ID: 16560

Type strain: Yes

Species: Nonomuraea longicatena

Strain Designation: K-252

Strain history: NRRL 15532 <-- Kyowa Hakko Kogyo Co., Ltd., Japan; K-252.

NCBI tax ID(s): 83682 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 12113

BacDive-ID: 16560

DSM-Number: 44817

keywords: genome sequence, 16S sequence, Bacteria

description: Nonomuraea longicatena K-252 is a bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 83682
  • Matching level: species

strain history

@refhistory
12113<- P. Kämpfer, Univ. Giessen <- NRRL <- Kyowa Hakko Kogyo Co., Ltd.; K-252
67770NRRL 15532 <-- Kyowa Hakko Kogyo Co., Ltd., Japan; K-252.

doi: 10.13145/bacdive16560.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiaceae
  • genus: Nonomuraea
  • species: Nonomuraea longicatena
  • full scientific name: Nonomuraea longicatena Chiba et al. 1999

@ref: 12113

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Nonomuraea

species: Nonomuraea longicatena

full scientific name: Nonomuraea longicatena Chiba et al. 1999

strain designation: K-252

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19709Beige10-14 daysISP 2
19709Beige10-14 daysISP 3
19709Beige10-14 daysISP 4
19709Beige10-14 daysISP 5
19709Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19709yesAerial MyceliumWhiteISP 2
19709noISP 3
19709noISP 4
19709noISP 5
19709noISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
12113https://www.dsmz.de/microorganisms/photos/DSM_44817-1.jpg© Leibniz-Institut DSMZ
12113https://www.dsmz.de/microorganisms/photos/DSM_44817.jpg© Leibniz-Institut DSMZMedium 65 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12113N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
12113GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19709ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19709ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19709ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19709ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19709ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
12113GYM+S MEDIUM (DSMZ Medium 214)yeshttps://mediadive.dsmz.de/medium/214Name: GYM+S MEDIUM (DSMZ Medium 214) Composition: Starch 20.0 g/l Agar 12.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
12113CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water

culture temp

@refgrowthtypetemperature
12113positivegrowth28
19709positiveoptimum28
67770positivegrowth28

Physiology and metabolism

compound production

  • @ref: 67770
  • compound: Compound K-252a (an inhibitor of protein kinase C)

observation

  • @ref: 67770
  • observation: quinones: MK-9(III,VIII-H4), MK-9(H2), MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1970917234glucose-
1970922599arabinose-
1970917992sucrose-
1970918222xylose-
1970917268myo-inositol-
1970929864mannitol-
1970928757fructose-
1970926546rhamnose-
1970916634raffinose-
1970962968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19709+-+-++-++++---+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19709-++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12113soilTokyoJapanJPNAsia
67770SoilTokyoJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121131Risk group (German classification)
197091Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12113
  • description: Nonomuraea longicatena gene for 16S rRNA
  • accession: AB018787
  • length: 1499
  • database: nuccore
  • NCBI tax ID: 83682

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nonomuraea longicatena NRRL15532; K-2522563366678draftimg83682
66792Nonomuraea longicatena JCM 11136651716968draftimg83682

GC content

  • @ref: 67770
  • GC-content: 71.7
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 12113

culture collection no.: DSM 44817, IFO 16462, JCM 11136, NBRC 16462, NRRL 15532

straininfo link

  • @ref: 85587
  • straininfo: 62566

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10555344Taxonomic re-evaluation of 'Nocardiopsis' sp. K-252T (= NRRL 15532T): a proposal to transfer this strain to the genus Nonomuraea as Nonomuraea longicatena sp. nov.Chiba S, Suzuki M, Ando KInt J Syst Bacteriol10.1099/00207713-49-4-16231999Actinomycetales/chemistry/*classification/cytology/genetics, Bacterial Typing Techniques, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Enzymology17396254Genetic organization of the biosynthetic gene cluster for the indolocarbazole K-252a in Nonomuraea longicatena JCM 11136.Kim SY, Park JS, Chae CS, Hyun CG, Choi BW, Shin J, Oh KBAppl Microbiol Biotechnol10.1007/s00253-007-0924-x2007Actinomycetales/*enzymology/*genetics, Carbazoles/*metabolism, Cloning, Molecular, Genetic Engineering, Indole Alkaloids/*metabolism, *Multigene Family, Streptomyces/enzymology/geneticsMetabolism
Phylogeny32501782Nonomuraea typhae sp. nov., an endophytic actinomycete isolated from the root of cattail pollen (Typha angustifolia L.).Peng C, Zhuang X, Wang Z, Gao C, Zhao J, Song J, Liu C, Shen YInt J Syst Evol Microbiol10.1099/ijsem.0.0042492020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Typhaceae/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
12113Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44817)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44817
19709Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44817.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
85587Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID62566.1StrainInfo: A central database for resolving microbial strain identifiers