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Institute of Molecular Genetics and Genetic Engineering, Vojvode Stepe 444a, PO Box 23, 11 010 Belgrade, Serbia
Correspondence
Branka Vasiljevic
vasiljb{at}eunet.yu
| ABSTRACT |
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Present address: Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, UK. ![]()
Present address: Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, Novum, SE-14186 Stockholm, Sweden. ![]()
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence of strain MS405T and the 16S–23S rDNA ITS region sequences of eight clones of strain MS405T are respectively DQ067287 and DQ067288–DQ067295.
Sequences of ITS variable regions in strain MS405T and electron micrographs of the strain are available as supplementary material with the online version of this paper.
| MAIN TEXT |
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Actinomycete strain MS405T was isolated by a serial dilution method (http://www.bio.com/protocolstools/protocol.jhtml?id=p2181) from soil samples collected at the Durmitor National Park, Serbia and Montenegro, as a producer of a secondary metabolite exhibiting an FK506-like immunosuppressant mechanism of action (Skoko et al., 2005
). The taxonomic status of strain MS405T was investigated using a combination of phenotypic and molecular systematic means, which were indispensable in placing strain MS405T within the genus Streptomyces. Polyphasic study of strain MS405T showed that this strain should be formally recognized as representing a novel species of the genus Streptomyces.
To investigate the phylogenetic relationships of strain MS405T, its almost-complete 16S rRNA gene sequence (1517 nt) was determined. Bacterial DNA was extracted by a method described previously (Hopwood et al., 1985
). The extracted DNA was subjected to PCR amplification with the bacteria-specific 16S rRNA primers 27f (Lane, 1991
) and 1392rev (Marchesi et al., 1998
). PCR amplification was performed as described by Marchesi et al. (1998)
. The 16S–23S ITS region, including the 3' end of the 16S rRNA gene, was amplified by PCR using primers AM45 (Mehling et al., 1995
) and L1 (Jensen et al., 1993
). PCR products were excised from the gel and purified using a QIAEXII gel extraction kit (Qiagen) according to the manufacturer's instructions. The purified product was then ligated to pMOSBlue vector according to the manufacturer's instructions (Amersham Pharmacia Biotech). Recombinant plasmid constructs were isolated using Qiagen minicolumns (QIAprep Spin Miniprep kit) and sequenced on an ALF Express sequencer using a Cy5-AutoRead kit (Amersham Biosciences) and the universal sequencing primers M13f and M13r.
16S rRNA gene sequence analysis was conducted using the BLAST network services provided by the NCBI (Altschul et al., 1997
) and the Ribosomal Database Project (RDP; http://rdp.cme.msu.edu) (Maidak et al., 2001
). Alignment was performed with the CLUSTAL W program (Thompson et al., 1994
). 16S rRNA gene sequences and 16S–23S ITS sequences were aligned against published sequences available in the DDBJ/GenBank/EMBL databases by the Knuc value of Kimura (1980)
, and phylogenetic trees were constructed by the neighbour-joining (Saitou & Nei, 1987
) and maximum-parsimony (Fitch, 1971
; Felsenstein, 1993
) algorithms contained in the PHYLIP package (version 3.5c; http://www.pasteur.fr). The topology of the phylogenetic tree was evaluated by the bootstrap resampling method of Felsenstein (1985)
with 1000 replicates. 16S rRNA gene sequence similarities were calculated using the EMBOSS:needle (global) method available at http://www.ebi.ac.uk.
Phylogenetic analysis, at the RDP (Maidak et al., 2001
), placed the strain within the evolutionary radiation encompassed by the genus Streptomyces, where the 16S rRNA gene sequence of Streptomyces aureus DSM 41785T was identified with the highest probability (0.969) as the closest matching sequence to MS405T. The analysis was supported by the neighbour-joining (Saitou & Nei, 1987
) and maximum-likelihood (Felsenstein, 1993
) methods. Comparing Streptomyces 16S rRNA gene sequences by phylogenetic tree algorithms, it was obvious that a subclade was formed (Fig. 1
) containing sequences of Streptomyces seoulensis IMSNU 21266T, S. aureus DSM 41785T, Streptomyces kanamyceticus DSM 40500T and strain MS405T. Within this subclade, strain MS405T formed a monophyletic line. This relationship was evident in evolutionary trees based on different treeing algorithms: neighbour-joining and DNADIST contained in the PHYLIP package (Felsenstein, 1993
), the maximum-parsimony algorithm (Fitch, 1971
; Felsenstein, 1993
), the maximum-likelihood (Felsenstein, 1993
) and BIONJ (Gascuel, 1997
) (Fig. 1
). The 16S rRNA gene sequence similarity values were 99.59 and 99.32 % between strain MS405T and S. aureus DSM 41785T and S. kanamyceticus DSM 40500T, over 1448 and 1477 nucleotides compared, respectively.
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Phylogenetic analyses based on the 16S–23S ITS regions placed strain MS405T close to Streptomyces scabiei isolate 87.79 (clone 79) (Fig. 2
), showing the limited usefulness of the 16S–23S ITS region in inferring the phylogenetic position of strain MS405T. The branching of MS405T 16S–23S ITS sequences in two closely related clades is probably due to indel events contained within sequences ITS2, ITS4, ITS6 and ITS7 that are absent in the other four sequences.
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The morphological characteristics of strain MS405T were assessed by transmission (model CM12; Philips) and scanning (model JSM-6460; JEOL) electron microscopy of 14-day-old cultures grown on NE medium at 30 °C (Skeggs et al., 1985
), following the procedure of O'Donnell et al. (1993)
. Cultural characteristics of strain MS405T were recorded after 14 days incubation according to the International Streptomyces Project (ISP) methods (Shirling & Gottlieb, 1966
). Colours were described according to the NBS-ISCC Color System (http://www.anthus.com).
Morphological observation of 14-day-old cultures grown on NE agar revealed aerial mycelium which consisted of straight chains of 10 or more rod-shaped, smooth-surfaced spores (0.5–0.9x1.0–1.5 µm) (Supplementary Fig. S1). The colour of the substrate mycelium was greenish grey on glycerol-asparagine agar (ISP5), where no diffusible pigment was detected, and medium grey on inorganic salts-starch agar (ISP4). Melanin was not produced on peptone-yeast extract-iron agar (ISP6) or tyrosine agar (ISP7) plates. Soluble dark-grey and dark-olive-green pigments were observed on ISP4 and NE, respectively. The phenotypic characteristics of strain MS405T and phylogenetically related Streptomyces species are shown in Table 1
. Biochemical, physiological and polymer degradation tests were performed as described previously (Seeley & VanDemark 1981
; Hopwood et al., 1985
; Williams et al., 1983
).
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The isomer type of diaminopimelic acid (DAP) in the peptidoglycan layer was determined by hydrolysing cells with 6 M HCl at 100 °C for 18 h and analysed by TLC as described previously (Rhuland et al., 1955
; Becker et al. 1965
; Hasegawa et al., 1983
), followed by ninhydrin staining (0.1 % w/v ninhydrin in acetone). Analysis showed that the cell wall contains LL-DAP, thereby indicating that strain MS405T exhibits cell-wall chemotype I (Lechevalier & Lechevalier, 1970
). Utilization of sugars or sugar alcohols as sole carbon sources was monitored in minimal medium containing M9 salts (6 g Na2HPO4, 3 g K2HPO4, 0.5 g NaCl, 1 g NH4Cl per litre, filter-sterilized) supplemented with 1 ml 1 M MgSO4, 1 ml 0.1 M CaCl2 and 1 % carbon source (w/v) (Miller, 1992
). Plates were incubated for 7 days at 30 °C. All media were adjusted to pH 7 prior to seeding.
The chemical, morphological and phylogenetic data suggest that strain MS405T represents a novel species when compared with type strains of species with validly published names within the genus Streptomyces. Thus, on the basis of this polyphasic taxonomic study, strain MS405T merits classification as the type strain of a novel species within the genus Streptomyces, and the name Streptomyces durmitorensis sp. nov. is proposed.
Description of Streptomyces durmitorensis sp. nov.
Streptomyces durmitorensis (dur.mi.tor.en'sis. N.L. masc. adj. durmitorensis pertaining to Durmitor, Serbia and Montenegro, where the type strain was isolated).
Gram-positive, non-acid-fast streptomycete that produces a yellowish-grey and a greenish-grey substrate mycelium and a greenish-yellow aerial spore mass on yeast extract-malt extract and glycerol-asparagine agars. Soluble pigments are not formed on oatmeal, yeast extract-malt extract or glycerol-asparagine agars, while dark-grey pigment is formed on inorganic salts-starch agar. Melanoid pigments are not formed on peptone/yeast extract/iron or tyrosine agars. Spore chains are rectiflexibiles, with 10 or more rod-shaped, smooth-surfaced spores (0.5–0.9x1.0–1.5 µm) per chain. Temperature range for growth is 10–37 °C with an optimum between 28 and 32 °C. The cell wall contains LL-DAP. Cellobiose, dextran, D-(–)-fructose, D-(+)-galactose, D-(+)-glucose, glycerol, D-(–)-mannitol, D-(+)-mannose,
-melibiose, D-(+)-raffinose, L-(+)-rhamnose, sucrose,
-trehalose and D-(+)-xylose are utilized for growth, but L-(+)-arabinose, myo-inositol,
-lactose,
-lactose, maltose and D-sorbitol are not utilized. Acid is produced from glucose. L-Alanine, L-arginine, L-cysteine, L-glycine, L-histidine, L-hydroxyproline, L-methionine, L-proline and L-valine are utilized as sole nitrogen sources, but L-asparagine, L-lysine, ornithine hydrochloride, L-phenylalanine and thiamine are not utilized. Nitrate is reduced to nitrite, gelatin is liquefied, xanthine is degraded, starch is not hydrolysed and aesculin and DNA are not degraded. Positive for nitrate reduction, catalase, extracellular protease, haemolysin (
-haemolysis) and urease. Negative for lecithinase and H2S and indole are not produced. Grows in the presence of NaCl (9 %, w/v) and thallous acetate (0.001 %, w/v), but not sodium azide (0.01 %, w/v), phenol (0.1 %, w/v) or potassium tellurite (0.001 %, w/v). Susceptible to apramycin (10 µg ml–1), kanamycin (5 µg ml–1), gentamicin (5 µg ml–1), tetracycline (10 µg ml–1), thiostrepton (10 µg ml–1), chloramphenicol (35 µg ml–1) and spectinomycin (90 µg ml–1), but resistant to ampicillin (100 µg ml–1), erythromycin (100 µg ml–1) and FK506 (100 µg ml–1). The type strain, MS405T, produces an immunosuppressant with an FK506-like mechanism of action. The G+C content of the DNA is 72 mol%. The type strain shows antimicrobial activity against Micrococcus luteus NCIMB 196 and Saccharomyces cerevisiae FAV 20, but not against Bacillus subtilis NCIMB 3610T, Candida albicans CBS 562, Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Saccharomyces cerevisiae FAS 20 or Staphylococcus aureus ATCC 25923.
The type strain, MS405T (=DSM 41863T =CIP 108995T), was isolated from a soil sample taken at the Durmitor National Park, Serbia and Montenegro.
| ACKNOWLEDGEMENTS |
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