16S–23S Ribosomal DNA Intergenic Spacer Regions in Cellulolytic Myxobacteria and Differentiation of Closely Related Strains

Nguimbi, Etienne; Li, Yuezhong; Gao, Beile; Li, Zhifeng; Wang, Bing; Wu, Zhihong; Yan, Bin; Qu, Yinbo; Gao, Pin

doi:10.1078/072320203322346119

Cited by 18 publications

(15 citation statements)

References 19 publications

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“…The known number of tRNA genes occurring in bacterial rrn operons varies from zero to five (4,5,12,17,27,44,46,48,50,51 (17,48). The sequence data analyzed from the 55 ISRs within these 5 C. difficile strains revealed they had a mosaic-like structure, as was also reported for the ISRs in Salmonella enterica, Haemophilus parainfluenzae, Staphylococcus aureus, Vibrio cholerae, Vibrio mimicus, Vibrio parahaemolyticus, Myxobacterium spp., and Acinetobacter baylyi (4,5,12,17,25,27,44,46,48,50,51). The highly mosaic nature of the C. difficile ISR is entirely consistent with the recent finding that the complete genome of C. difficile is also mosaic in nature, with 11% of the genome comprised of mobile genetic elements that in many cases contain repetitive sequences (59).…”

Section: Discussionmentioning

confidence: 79%

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The Mosaic Nature of Intergenic 16S-23S rRNA Spacer Regions Suggests rRNA Operon Copy Number Variation in Clostridium difficile Strains

Sadeghifard

Gürtler

Beer

et al. 2006

Appl Environ Microbiol

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Clostridium difficile is a major spore-forming environmental pathogen that causes serious health problems in patients undergoing antibiotic therapy. Consequently, reliable and sensitive methods for typing individual strains are required for epidemiological and environmental studies. Ribotyping is generally considered the best method, but it fails to account for sequence diversity which might exist in intergenic 16S-23S rRNA spacer regions (ISRs) within and among strains of this organism. Therefore, this study was undertaken to compare the sequence of each individual ISR in five strains of C. difficile to explore the extent of this diversity and see whether such information might provide the basis for more sensitive and discriminatory strain typing methods. After targeted PCR amplification, cloning, and sequencing, the diversity of the ISRs was used as a measure of rRNA operon copy number. In C. difficile strains 630, ATCC 43593, A, and B, 11, 11, 7, and 8 ISR length variants, respectively, were found (containing different combinations of sequence groups [i to xiii]), suggesting 11, 11, 7, and 8 rrn copies in the respective strains. Many ISRs of the same length differed markedly in their sequences, and some of these were restricted in occurrence to a single strain. Most of these ISRs did not contain any tRNA genes, and only single copies of the tRNA Ala gene were found in those that did. The presence of ISR sequence groups (i to xiii) varied between strains, with some found in one, two, three, four, or all five strains. We conclude that the intergenic 16S-23S rRNA spacer regions showed a high degree of diversity, not only among the rrn operons in different strains and different rrn copies in a single strain but also among ISRs of the same length. It appears that C. difficile ISRs vary more at the inter-and intragenic levels than those of other species as determined by empirical comparison of sequences. The precise characterization of these sequences has demonstrated a high level of mosaic sequence block rearrangements that are present or absent in multiple strain-variable rrn copies within and between five different strains of C. difficile.

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Section: Discussionmentioning

confidence: 79%

“…Many authors have compared ISRs between different species and strains of a single bacterial species (15,17,33,44,46). In some cases the ISR diversity between species of a genus is lower than the diversity seen between the strains of C. difficile examined here.…”

Section: Discussionmentioning

confidence: 99%

The Mosaic Nature of Intergenic 16S-23S rRNA Spacer Regions Suggests rRNA Operon Copy Number Variation in Clostridium difficile Strains

Sadeghifard

Gürtler

Beer

et al. 2006

Appl Environ Microbiol

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“…While the 16S rDNA sequence is a good tool for inferring inter-and intrageneric relationships, 16S-23S rRNA spacer sequence comparisons provide information concerning the intraspecific links and allow researchers to detect recently diverged species [21]. Thus, ITS or ISR sequences have been proposed to be a useful supplement when 16S rRNA gene sequences exhibit insufficient diversity to differentiate closely related species [11,31]. In this study, the 398-nt 16S~23S rRNA ISR sequence of strain SCY114 was PCR amplified and sequenced ( GenBank accession No.…”

Section: Structural Elucidation Of the Antifungal Compoundmentioning

confidence: 99%

Streptomyces scabiei subsp. xuchangensis, A NOVEL STREPTOMYCETE ISOLATE FOR STAUROSPORINE PRODUCTION AND A WHEAT TAKE-ALL CONTROL AGENT

Cai-yi¹,

ZHENG²,

Shen³

et al. 2012

Int J of Micr Res

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Abstract-The streptomycete strain SCY114 was isolated from a soil sample of Xuchang in Henan province, China. It possessed smooth grey spores borne in rectiflexible and spiral chains and was capable of using all of the International Streptomyces Project sugars. The melting temperature and G+C content were 81.8℃ and 61.6 mol%, respectively. The level of 16S rRNA gene sequence similarity between strain SCY114 and S. scabies ATCC49173 was 99.8%. However, the values of DNA-DNA relatedness between strain SCY114 and S. scabies ATCC49173 was 65.2%, and the strain SCY114 did not exhibit pathogenicity towards potato plants. Based on the phenotypic and genotypic evidence, strain SCY114 was identified as a subspecies of the Streptomyces scabiei, for which the name Streptomyces scabiei subsp. xuchangensis is proposed. Strain SCY114 strongly inhibited the in vitro mycelial growth of Gaeumannomyces graminis var. tritici as well as various other plant pathogenic fungi. The filtered culture broth of strain SCY114 was substantially more effective at controlling wheat take-all compared to the silthiofam, and the disease was reduced by 78.2%. An antifungal antibiotic was isolated from the fermentation broth of strain SCY114 using a series of chromatographic procedures. The molecular formula of the antibiotic was determined to be C28H26N4O3, and on the basis of the NMR data, the antibiotic was confirmed to be staurosporine.

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“…The molecular formula was determined to be C 26 H 39 NO 7 (Table 1). The 13 C NMR spectrum of 1 displayed 26 carbon signals for five methyl, six methylene, nine methine and six quaternary carbon atoms, including a carbonyl carbon at d 171.9 (C-1), together with the 1 H NMR spectrum clearly revealed a typical epothilone structure, including the presence of a thiazole ring, a carbon-carbon double bond, an epoxy function and a carboxyl carbonyl group (Table 1).…”

mentioning

confidence: 99%

“…7 Epohtilones A 9 (3) (3.0 mg), A (4) (90 mg), B (250 mg) and C (20 mg) were isolated from the 70 l fermentation extract by repeated column chromatography (Sephadex LH-20, RP-18 and silica gel, Sephadex, Uppsala, Sweden). The polar epothilone-containing fractions were separated by HPLC (Agilent 1200 instrument, Agilent, Palo Alto, CA, USA; C 18 column: Zorbax SB-C18, Agilent, 4.6Â250 mm, 5 mm), eluting with 65% methanol at a flow rate of 1.0 ml min À1 to yield compound 1 (t R 7.8 min, 2.0 mg) and 2 (t R 10.9 min, 0.8 mg).…”

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confidence: 99%

Two 18-membered epothilones from Sorangium cellulosum So0157-2

Chen

Liu

et al. 2010

J Antibiot

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Epothilones are 16-membered ring macrolides originally isolated from the bacterium Sorangium cellulosum Soce90, 1,2 which were found to kill dividing cells by stabilizing microtubules. 3 Previously, epothiloneproducing strains of the genus Sorangium were isolated and screened in our laboratories. We found that one strain, designated S. cellulosum So0157-2, was able to produce epothilones. 4 The production of epothilones A and B by S. cellulosum So0157-2 was optimized to industrial scales. 5 Recently, five new epothilone glycoside derivatives were isolated from this strain. 6 As a part of our ongoing search for new epothilones from S. cellulosum So0157-2, we focused on the minor and polar components of this strain produced in large-scale fermentations.The strain S. cellulosum So0157-2 was cultivated in 70 l of M26 medium. 7 Epohtilones A 9 (3) (3.0 mg), A (4) (90 mg), B (250 mg) and C (20 mg) were isolated from the 70 l fermentation extract by repeated column chromatography (Sephadex LH-20, RP-18 and silica gel, Sephadex, Uppsala, Sweden). The polar epothilone-containing fractions were separated by HPLC (Agilent 1200 instrument, Agilent, Palo Alto, CA, USA; C 18 column: Zorbax SB-C18, Agilent, 4.6Â250 mm, 5 mm), eluting with 65% methanol at a flow rate of 1.0 ml min À1 to yield compound 1 (t R 7.8 min, 2.0 mg) and 2 (t R 10.9 min, 0.8 mg). Their structures were established as epothilone-type 18-membered ring macrolides, named epothilones M (1) and N (2). In this study, we describe structure elucidation and cytotoxic activity of these two new epothilones.Compound 1 was isolated as a white powder. Table 1). The 13 C NMR spectrum of 1 displayed 26 carbon signals for five methyl, six methylene, nine methine and six quaternary carbon atoms, including a carbonyl carbon at d 171.9 (C-1), together with the 1 H NMR spectrum clearly revealed a typical epothilone structure, including the presence of a thiazole ring, a carbon-carbon double bond, an epoxy function and a carboxyl carbonyl group (Table 1). However, compared with epothilone A (4), 1,2 1 had one less methyl and one more oxymethylene group as a substitutent at the carbon-carbon double bond. Among the various epothilone derivatives, the only known oxymethylenesubstituted compounds are represented by epothilones A 9 and C 9 . 8 Indeed, the structure of epothilone A 9 could explain the 13 C NMR spectrum of 1. However, the 1 H NMR chemical shifts of the oxymethylene protons (H-17) were observed at d 5.07 and 5.45 in 1, but at d 4.11 and 4.49 in epothilone A 9, 8 respectively. This difference could be the effect of esterification, indicating that the hydroxymethyl hydroxyl group (17-OH) of epothilone A 9 could be esterified in 1. Moreover, in our work, epothilone A 9 (3) was isolated too. The unambiguous NMR data assignments for 3 provided further support for this esterification (Table 1). The heteronuclear multiple-bond correlations from the oxymethylene protons (H-17) at d 5.07 and 5.45 to the carbonyl group at d 171.9 (C-1) indicated the presence of an ester bond b...

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16S–23S Ribosomal DNA Intergenic Spacer Regions in Cellulolytic Myxobacteria and Differentiation of Closely Related Strains

Cited by 18 publications

References 19 publications

The Mosaic Nature of Intergenic 16S-23S rRNA Spacer Regions Suggests rRNA Operon Copy Number Variation in Clostridium difficile Strains

The Mosaic Nature of Intergenic 16S-23S rRNA Spacer Regions Suggests rRNA Operon Copy Number Variation in Clostridium difficile Strains

Streptomyces scabiei subsp. xuchangensis, A NOVEL STREPTOMYCETE ISOLATE FOR STAUROSPORINE PRODUCTION AND A WHEAT TAKE-ALL CONTROL AGENT

Two 18-membered epothilones from Sorangium cellulosum So0157-2

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