[Show abstract][Hide abstract] ABSTRACT: Two Gram-negative, lack of motility, catalase- and oxidase- positive, designated MS7T isolated from freshwater in Trabzon, Turkey and its phylogenetic position was investigated using a polyphasic approach. The strain grew optimally at 28 °C and pH 7.5 and in the presence of 2.0 % NaCl. 16S rRNA gene sequence analysis revealed that the strain belonged to the genus Algoriphagus; strain MS7T showed highest sequence similarity to strain Algoriphagus alkaliphilus 97.31 %, Algoriphagus terrigene 96.86 %, Algoriphagus jejuensis 96.29 %, Algoriphagus boritolerans 96.14 % and A. aquatilis 95.88 %. The major fatty acids of strain MS7T were iso-C15 : 0 (30.14%) and and summed future 9 (10-methyl C16 : 0 and/or iso-C17 : 1 ω9c 18.75 %). Polar lipid analysis revealed a phosphatidylethanolamine, a variety of unidentified lipids, unidentified aminophospolipid, unidentified phospholipid and unidentified aminolipid. The major isoprenoid quinone was MK-7. The DNA G+C content of MS7T was 41.6 mol%, a value consistent with that of members of the genus Algoriphagus. The level of DNA-DNA relatedness between strain MS7T and Algoriphagus alkaliphilus AC74T was 41 %, which is clearly below the 70 % threshold accepted for species delineation. Thus, our results support the placement of strain MS7T within a separate and previously unrecognized species. Based on these data, the strain is considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus trabzonensis sp. nov. is proposed. The type strain is MS7T (=NCCB 100372T=LMG 26290T).
International Journal of Systematic and Evolutionary Microbiology 04/2015; DOI:10.1099/ijs.0.000246 · 2.80 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A Gram-staining-negative, catalase- and oxidase- positive, strictly aerobic, rod-shaped bacterial strain isolated from fresh water in Trabzon, Turkey and designated MK3T was characterized by phenotypic and molecular methods in order to determine its phylogenetic position. On the basis of 16S rRNA gene sequence similarity, strain MK3T was shown to belong to the genus Flavobacterium, being most closely related to Flavobacterium ceti CECT 7184 (93.6 %). Sequence similarity with other validly named Flavobacterium species was less than 91.6%. Phenotypic and chemotaxonomic data supported the affiliation of strain MK3T to the genus Flavobacterium. The only menaquinone was MK-6; the major fatty acids were iso-C15: 0 (45.2%), summed feature 9 (C16:0 10-methyl and/or iso C17:1ω9c; 20.4%) and summed feature 3 (C16:1ω7c and/or C16:1ω6c; 13.3 %) and the major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid and two unidentified phospholipids. The G+C content of the genomic DNA was 38.6 %mol. The results of physiological and biochemical tests allowed strain MK3T to be distinguished phenotypically from Flavobacterium ceti CECT 7184T. Strain MK3T, therefore, represents a novel species of the genus Flavobacterium, for which the name Flavobacterium anatoliense sp. nov. is proposed. An emended description of Flavobacterium ceti is also proposed. The type strain is MK3T (=LMG 26441T =NCCB 100384T ).
International Journal of Systematic and Evolutionary Microbiology 10/2012; 63(Pt 6). DOI:10.1099/ijs.0.040394-0 · 2.80 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The gene encoding a xylanase from Geobacillus sp. 71 was isolated, cloned, and sequenced. Purification of the Geobacillus sp 7.1 xylanase, XyzGeo71, following overexpression in E. coli produced an enzyme of 47 kDa with an optimum temperature of 75°C. The optimum pH of the enzyme is 8.0, but it is active over a broad pH range. This protein showed the highest sequence identity (93%) with the xylanase from Geobacillus thermodenitrificans NG80-2. XyzGeo71 contains a catalytic domain that belongs to the glycoside hydrolase family 10 (GH10). XyzGeo71 exhibited good pH stability, remaining stable after treatment with buffers ranging from pH 7.0 to 11.0 for 6 h. Its activity was partially inhibited by Al(3+) and Cu(2+) but strongly inhibited by Hg(2+). The enzyme follows Michaelis-Menten kinetics, with K(m) and V(max) values of 0.425 mg xylan/ml and 500 μmol/min.mg, respectively. The enzyme was free from cellulase activity and degraded xylan in an endo fashion. The action of the enzyme on oat spelt xylan produced xylobiose and xylotetrose.
World Journal of Microbiology and Biotechnology (Formerly MIRCEN Journal of Applied Microbiology and Biotechnology) 05/2012; 28(5):1981-8. DOI:10.1007/s11274-011-1000-3 · 1.35 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A facultatively anaerobic, thermophilic, xylanolytic bacterium was isolated from a sample collected from the Diyadin Hot Springs,
Turkey. According to morphological, biochemical and molecular identification, this new strain was suggested to be representative
of the Anoxybacillus pushchinoensis and it was designated as Anoxybacillus pushchinoensis strain A8. It exhibited 97% similarity to 16S rRNA gene sequence of A. pushchinoensis and 77% DNA homology by DNA-DNA hybridization studies. Q-sepharose and CM-sepharose chromatography was used to purify an
extracellular xylanase to >90% purity from this species. The enzyme had a molecular mass of approximately 83 kDa. The enzyme
showed optimum activity at pH 6.5 and it was 96% stable over a broad pH range of 6.5–11 for 24 hours. The enzyme had optimum
activity at 55°C and it was 100% stable at temperature between 50–60°C up to 24 hours. Kinetic characterization of the enzyme
was performed at temperature optima (55°C) and Vmax and K
m were found to be 59.88 U/mg protein and 0.909 mg/mL, respectively. Oat spelt xylan but not xylooligosaccharides was degraded
by the enzyme and xylose was the only product detected from oat xylan degradation. This suggested that the enzyme was an exo-acting
[Show abstract][Hide abstract] ABSTRACT: The gene, AbfAC26Sari, encoding an alpha-L-arabinofuranosidase from Anoxybacillus kestanbolensis AC26Sari, was isolated, cloned, sequenced, and characterized. On the basis of amino acid sequence similarities, this 57-kDa enzyme could be assigned to family 51 of the glycosyl hydrolase classification system. Characterization of the purified recombinant alpha-L-arabinofuranosidase produced in Escherichia coli BL21 revealed that it is active at a broad pH range (pH 4.5 to 9.0) and at a broad temperature range (45-85 degrees C) and it has an optimum pH of 5.5 and an optimum temperature of 65 degrees C. Kinetic experiment at 65 degrees C with p-nitrophenyl alpha-L-arabinofuranoside as a substrate gave a Vmax and Km values of 1,019 U/mg and 0.139 mM, respectively. The enzyme had no apparent requirement of metal ions for activity, and its activity was strongly inhibited by 1 mM Cu2+ and Hg2+. The recombinant arabinofuranosidase released L-arabinose from arabinan, arabinoxylan, oat spelt xylan, arabinobiose, arabinotriose, arabinotetraose, and arabinopentaose. Endoarabinanase activity was not detected. These findings suggest that AbfAC26Sari is an exo-acting enzyme.
[Show abstract][Hide abstract] ABSTRACT: The chitinase B gene (chiB65) ofBacillus licheniformis A1 (BlicA1) isolated from Diyadin hotspring in Turkey was cloned and sequenced. The gene is 1779 bp long and encodes a protein 592
amino acids with a 35-amino acid signal peptide at N-terminal. The gene has 99% percent similarity tochiB gene ofBacillus licheniformis under the GenBank number AY205293. The gene without signal peptide was overexpressed inEscherichia coli and the recombinant protein purified by nickel affinity chromatography. The activity of enzyme was shown on SDS-PAGE with
the flourogenic substrate 4-methylumbelliferyl β-D-N,N′-diacetylchitobioside. Kinetic characterisation of the enzyme was performed at 65 °C by using chromogenic substratep-nitrophenylN,N′-diacetyl-β-D-chitobioside, andK
m and Vmax were found to be 0.02 μM and 1017 U/mg protein, respectively. Enzyme has maximal activity at pH 6.0 and was stable over a
broad pH range of 5.0–9.0 for 24 h at room temperature and 4 h at 65 °C. Enzyme was 60% stable at 65 °C for 1.5 h. The inhibition
or activation of some substances on the activity of enzyme was determined. High kinetic properties of enzyme open the possibility
of an extensive structural and enzyme-substrate interaction studies.
Annals of Microbiology 06/2008; 58(2):245-251. DOI:10.1007/BF03175324 · 1.04 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Some hot springs located in the west of Turkey were investigated with respect to the presence of thermophilic microorganisms. Based on phenotyping characteristics and 16S rRNA gene sequence analysis, 16 of the isolates belonged to the genus Geobacillus and grew optimally at about 60 degrees C on nutrient agar. 16S rRNA gene sequence analysis showed that these isolates resembled Geobacillus species by > or = 97%, but SDS-PAGE profiles of these 16 isolates differ from some of the other species of the genus Geobacillus. However, it is also known that analysis of 16S rRNA gene sequences may be insufficient to distinguish between some species. It is proposed that recN sequence comparisons could accurately measure genome similarities for the Geobacillus genus. Based on recN sequence analysis, isolates 11, IT3, and 12 are strains of G stearothermophilus; isolate 14.3 is a strain of G thermodenitrificans; isolates 9.1, IT4.1, and 4.5 are uncertain and it is required to make further analysis. The presence of xylanase and arabinofuranosidase activities, and their optimum temperature and pH were also investigated. These results showed that 7 of the strains have both xylanase and arabinofuranosidase activities, 4 of them has only xylanase, and the remaning 5 strains have neither of these activities. The isolates 9.1, 7.1, and 3.3 have the highest temperature optima (80 degrees C), and 7.2, 9.1, AO4, 9.2, and AO17 have the highest pH optima (pH 8) of xylanase. Isolates 7.2, AO4, AC15, and 12 have optimum arabinofuranosidase activities at 75 degrees C, and only isolate AC 15 has the lowest pH of 5.5.
Journal of Microbiology and Biotechnology 08/2007; 17(8):1262-70. · 1.32 Impact Factor