Nucleotide Sequence Accession Number Research Articles

Correction for Sakwinska et al., "Nasopharyngeal Microbiota in Healthy Children and Pneumonia Patients".

Volume 52, no. 5, p. 1590–1594, 2014, [https://doi.org/10.1128/JCM.03280-13][1]. Page 1591: The following paragraph should appear at the end of the Materials and Methods section. Nucleotide sequence accession number. Raw 454 sequencing data have been deposited in the NCBI Short Read Archive under

Relationship between plasmid occurrence and antibiotic resistance in Myroides odoratimimus SKS05-GRD isolated from raw chicken meat

Fifteen flavobacterium strains were isolated from raw chicken meat, raw goat meat and poultry soil in Coimbatore, Tamil Nadu. Most of the isolates developed yellow pigmented colonies with mucoid-spreading edges on food flavobacterium medium. The flavobacteria were Gram-negative rods and failed to produce indole and were non-fermentative. Moreover, they produced a rich array of enzymes such as amylase, lipase, catalase, urease, gelatinase, DNase, and oxidase. Phylogenetic analyses of the strain SKS05-GRD based on 16S rRNA gene sequences revealed the bacterium as Myroides odoratimimus (nucleotide sequence accession number JQ178355). Antimicrobial susceptibility test for M. odoratimimus SKS05-GRD and other strains were assessed by disc diffusion method. M. odoratimimus SKS05-GRD showed wide resistance to the antibiotics such as amikacin, ampicillin, cefadroxil, cefoperazone, ceftazidine, ceftriaxone, netillin and gentamicin. M. odoratimimus was subjected to plasmid isolation and plasmid curing to seek the relationship between plasmid and antibiotic resistance. Plasmid curing was done by using ethidium bromide and was found to be effective at 300 and 500μg/ml. Assessment of antibiotic sensitivity of M. odoratimimus SKS05-GRD showed sensitivity to amikacin, gentamicin and kanamycin confirming that resistance to these three antibiotics is plasmid mediated and other antibiotic resistance are chromosomal mediated.

A salt lake extremophile, Paracoccus bogoriensis sp. nov., efficiently produces xanthophyll carotenoids

A Gram-negative obligate alkaliphilic bacterium (BOG6T) that secretes carotenoids was isolated from the outflow of Lake Bogoria hot spring located in the Kenyan Rift Valley. The bacterium is motile by means of a polar flagellum, and forms red colonies due to the production of xanthophyll carotenoid pigments. 16S rRNA gene sequence analysis showed this strain to cluster phylogenetically within the genusParacoccus. Strain BOG6T is aerobic, positive for both catalase and oxidase, and non- methylotrophic. The major fatty acid of the isolate is C18: 1w7c. It accumulated polyhydroxybutyrate granules. Strain BOG6T gave astaxanthin yield of 0.4 mg/g of wet cells indicating a potential for application in commercial production of carotenoids. On the basis of its genotypic characteristics, fatty acid composition and physiological reaction profiles, it is proposed that the isolate may be assigned to the genus Paracoccus as Paracoccus bogoriensis sp. nov. The type strain is BOG6T (=DSM16578 =LMG22798). The GenBank 16S rDNA nucleotide sequence accession number is AJ580352. Key words: Paracoccus bogoriensis, alpha-proteobacteria, alkaliphile, xanthophylls, astaxanthin, extremophile, carotenoids.

Cloning and Characterization of a Streptomyces Single Module Type Non-ribosomal Peptide Synthetase Catalyzing a Blue Pigment Synthesis

In the present study, we cloned a gene, designated bpsA, which encodes a single module type non-ribosomal peptide synthetase (NRPS) from a D-cycloserine (DCS)-producing Streptomyces lavendulae ATCC11924. A putative oxidation domain is significantly integrated into the adenylation domain of the NRPS, and the condensation domain is absent from the module. When S. lividans was transformed with a plasmid carrying bpsA, the transformed cells produced a blue pigment, suggesting that bpsA is responsible for the blue pigment synthesis. However, to produce the blue pigment in Escherichia coli, the existence of the 4'-phosphopantetheinyl transferase (PPTase) gene from Streptomyces was necessary, in addition to bpsA. The chemical structure of the pigment was determined as 5,5'-diamino-4,4'-dihydroxy-3,3'-diazadiphenoquinone-(2,2'), called indigoidine. The bpsA gene product, designated BPSA, was overproduced in an E. coli host-vector system and purified to homogeneity, demonstrating that the recombinant enzyme prefers L-Gln as a substrate. The in vitro experiment using L-Gln also showed that the blue pigment was formed by the purified BPSA only when the enzyme was phosphopantetheinylated by adding a Streptomyces PPTase purified from E. coli cells. Each site-directed mutagenesis experiment of Lys(598), Tyr(601), Ser(603), and Tyr(608), which are seen in the oxidation domain of BPSA, suggests that these residues are essential for the binding of FMN to the protein and the synthesis of the blue pigment.

Propionicicella superfundia gen. nov., sp. nov., a chlorosolvent-tolerant propionate-forming, facultative anaerobic bacterium isolated from contaminated groundwater

A novel strain, designated as BL-10 T, was characterized using a polyphasic approach after isolation from groundwater contaminated by a mixture of chlorosolvents that included 1,1,2-trichloroethane, 1,2-dichloroethane, and vinyl chloride. Stain BL-10 T is a facultatively anaerobic bacterium able to ferment glucose to form propionate, acetate, formate, lactate, and succinate. Fermentation occurred in the presence of 1,2-dichloroethane and 1,1,2-trichloroethane at concentrations to at least 9.8 and 5.9 mM, respectively. Cells are Gram-positive, rod-shaped, non-motile, and do not form spores. Oxidase and catalase are not produced and nitrate reduction did not occur in PYG medium. Menaquinone MK-9 is the predominant respiratory quinone and meso-diaminopimelic acid is present in the cell wall peptidoglycan layer. Major cellular fatty acids are C 15:0, iso C 16:0, and anteiso C 15:0. Genomic DNA G+C content is 69.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed strain BL-10 T to fall within the radiation of genera Propionicimonas and Micropruina. On the basis of the results obtained in this study, it is proposed that strain BL-10 T should be classified as a novel taxon, for which the name Propionicicella superfundia gen. nov., sp. nov. is proposed. The type strain of Propionicicella superfundia is BL-10 T (=ATCC BAA-1218 T, =LMG 23096 T). 1 1 Nucleotide sequence accession number. Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number DQ176646.

Molecular cloning and expression of a novel family A endoglucanase gene from Fibrobacter succinogenes S85 in Escherichia coli.

A Fibrobacter succinogenes S85 gene that encodes endoglucanase hydrolysing CMC and xylan was cloned and expressed in Escherichia coli DH5 by using pUC19 vector. Recombinant plasmid DNA from a positive clone hydrolysing CMC and xylan was designated as pCMX1, harboring 2,043 bp insert. The entire nucleotide sequence was determined, and an open-reading frame (ORF) was deduced. The nucleotide sequence accession number of the cloned gene sequence in Genbank is U94826. The endoglucanase gene cloned in this study does not have amino sequence homology to the other endoglucanase genes from F. succinogenes S85, but does show sequence homology to family 5 (family A) of glycosyl hydrolases from several species. The ORF encodes a polypeptide of 654 amino acids with a measured molecular weight of 81.3 kDa on SDS-PAGE. Putative signal sequences, Shine-Dalgarno-type ribosomal binding site and promoter sequences (-10) related to the consensus promoter sequences were deduced. The recombinant endoglucanase by E. coli harboring pCMX1 was partially purified and characterized. N-terminal sequences of endoglucanase were Ala-Gln-Pro-Ala-Ala, matched with deduced amino sequences. The temperature range and pH for optimal activity of the purified enzyme were 55 approximately 65 degrees C and 5.5, respectively. The enzyme was most stable at pH 6 but unstable under pH 4 with a K(m) value of 0.49% CMC and a V(max) value of 152 U/mg.

Cloning and expression of β-glucosidase from Flavobacterium meningosepticum: a new member of family B β-glucosidase

A β-glucosidase gene from Flavobacterium meningosepticum has been cloned and expressed in Escherichia coli. The entire nucleotide sequence was determined and analyzed. An open-reading frame of 2,178 bp encoding a polypeptide of 726 amino acids with a calculated M r of 79,952 was derived from the sequence. The coding region is flanked by a putative promoter and transcription terminator sequences. The nucleotide sequence accession number of the complete gene sequence in Genbank is AF015915. Based on the comparison of amino acid sequences, this enzyme is classified as a family B β-glucosidase and is highly homologous with sequences from Clostridium thermocellum, Kluyvermyces fragilis, and Agrobacterium tumefaciens. The cloned enzyme was purified to near homogeneity by ammonium sulfate fractionation (35 ∼ 75%) and chromatography on a cation-exchanged column at pH 6.9. This expressed β-glucosidase has optimum activity at pH 4.2 ∼ 5.0 and 50°C and is stable in the pH range of 5.0 ∼ 8.1 at 25°C. It showed a high specificity on the glycone portion of aryl-β- d-glycosides. All of these characteristics are highly consistent with those of the native β-glucosidase.