Analysis of a ribosomal RNA operon in the actinomycete Frankia

Normand, Philippe; Cournoyer, Benoît; Simonet, Pascal; Nazaret, Sylvie

doi:10.1016/0378-1119(92)90612-s

Cited by 144 publications

(90 citation statements)

References 20 publications

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“…The 5' and 3' ends of the 16s-23s ITS regions were deduced from the 3' ends of the 16s rDNAs and the 5' ends of the 23s rDNAs of B. subtilis (5), Frankia sp. (21), and some Streptomyces species (2, 10, 22, 31, 37) described previously. The data show that S. viridis strains have the shortest 16S-23s ITS regions.…”

Section: Resultsmentioning

confidence: 99%

“…The oligonucleotide primer annealing at the region close to the 5' end of 23s rDNA (primer 23SR) was designed by using 5' sequences of the 23s rRNA genes of Bacillus subtilis (5), Frankia sp. (21), and some Streptomyces species (10,22,31), and its sequence was 5'-AGGCATCCACCGTGCGCCCT-3' (positions 34 to 14 [E. coli 23s rRNA numbering]). The PCR product containing the 23S-5s intergenic spacer was amplified with primers corresponding to the conserved regions of 23s rDNA and 5s rDNA.…”

Section: Methodsmentioning

confidence: 99%

“…The sequence of the oligonucleotide primer annealing to 23s rDNA (primer 23SF) was 5'-GCGAAA'MCCITGTCGGGTA-3' (positions 1933 to 1952 [E. coli 23s rRNA numbering]), which was shown to be conserved from an alignment of the 23s rRNA sequences of B. subtilis (5), Frankia sp. (21), and some Streptomyces species (10,22,31). The sequence of the oligonucleotide primer annealing to 5s rDNA (primer 5SR) was 5'-TGTCCTA CTCTCCCAC-3' (positions 109 to 94 [E. coli 5s rRNA numbering]), and this primer was selected from an alignment of 5s rRNA sequences of Succharomonospora species obtained from the GenBank database.…”

Section: Methodsmentioning

confidence: 99%

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Inter- and Intraspecific Genetic Analysis of the Genus Saccharomonospora with 16S to 23S Ribosomal DNA (rDNA) and 23S to 5S rDNA Internally Transcribed Spacer Sequences

Yoon

Lee²,

Kim³

et al. 1997

International Journal of Systematic Bacteriology

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In order to clarify interspecific relationships and to investigate the intraspecific phylogenetic structure of the genus Saccharomonospora, 16s to 23s ribosomal DNA (16s-23s) and 23s to 5s ribosomal DNA (23s-5s) internally transcribed spacers (ITSs) were used for sequence analyses. The 16s-23s and 23s-5s ITSs from 22 Saccharomonospora strains were amplified by PCR and directly sequenced. The average levels of nucleotide similarity of the 16s-23s and 23s-5s ITSs for the four valid species were 87.6% f 3.9% and 83% +-2.2%, respectively. For the most part, intraspecific sequence differences were not found in the two ITSs; the only exception was Saccharomonospora ghuca K194, which differed from other S. ghuca strains by 1 bp in the 23s-5s ITS. The Sacchuromonospora viridis strains had a smaller 16s-23s ITS region than the other strains, which may be useful for differentiating these organisms from other Saccharomonospora species. The characteristics of the two ITS regions make them more useful than 16s rRNA sequences as a tool for defining and identifying Saccharomonospora strains. However, Sacchuromonospora azurea K161T had two types of 23s-5s ITSs; rrnB, separated by XhoI digestion, had two additional nucleotides inserted between positions 52 and 55. Most of the 16s-23s and 23s-5s ITS sequences of S. azurea K161T and strains of "Saccharomonospora caesia" were identical; the only exception was rrnB in S. azurea K161T. The lengths and levels of sequence divergence of the two ITSs of Saccharomonospora sp. strain KlSO were different from the lengths and levels of sequence divergence of the ITSs of other species. These findings suggest that a taxonomic revision of the genus Saccharomonospora is necessary. Two trees based on 16s-23s and 23s-5s ITS sequences revealed distinct interspecific relationships in the genus Saccharomonospora.The genus Saccharomonospora was proposed by Nonomura and Ohara (20) for monosporic actinomycetes containing meso-diaminopimelic acid, arabinose, and galactose in the cell wall peptidoglycan (wall chemotype IV sensu Lechevalier and Lechevalier [ 181). Representatives of this genus form nonfragmenting, branched mycelia and develop aerial hyphae that bear single spores. The additional physical and chemical markers that characterize the genus have been described elsewhere The original type species of the genus is Saccharomonospora viridis (20). In addition to S. viridis, three Saccharomonospora species, Saccharomonospora azurea (24), Saccharomonospora cyanea (25), and Saccharomonospora glauca (7), have been validly described. Although "Saccharomonospora caesia" was proposed by Greiner-Mai et al. (8) as a fifth taxon for strains previously classified as Micropolyspora caesia (9, 13), this organism was not included on the Approved Lists of Bacterial Names (28) and has not been validly published on subsequent Approved Lists or Validation Lists. The results of recent numerical phenetic studies (11) and results obtained by nucleic acid techniques (12,(39)(40)(41) suggest that the strains of "S. caesi...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Inter- and Intraspecific Genetic Analysis of the Genus Saccharomonospora with 16S to 23S Ribosomal DNA (rDNA) and 23S to 5S rDNA Internally Transcribed Spacer Sequences

Yoon

Lee²,

Kim³

et al. 1997

International Journal of Systematic Bacteriology

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“…Primers used for the amplification of the 16S rRNA sequence were FGPS 6 and FGPS 1509 (Normand et al 1992). The PCR reaction mixture of 25 μl contained 1 μl of cell suspension, 0.5 μl of 5.5U/μl Taq DNA polymerase (Invitrogen Life Technologies), 0.5 μl of each 50 μM primer, 5 μl of polymerisation buffer containing dNTPs (Fisher Biotech, Australia), 15 μl of UltraPure grade water (Fisher Biotech, Australia) and 2.5 μl of 17 mM MgCl 2 (Promega Corp.).…”

Section: Assessing the Timing Of Nodule Initiation And Nodule Developmentioning

confidence: 99%

“…The purified product was used as DNA template in the sequencing reactions. Sequencing primers used in this study were FGPS 6 and FGPS 1509 (Normand et al 1992) and the internal primers 800 F, 1,100 F, 520R and 820R (Yanagi and Yamasato 1993). For each primer the following sequencing reaction was prepared: 4 μl of purified DNA template, 4 μl of Big Dye Terminator (version 3.1), 1 μl of 3.2 pmole/l primer and deionised water to make up a final volume of 10 μl per reaction.…”

Section: Assessing the Timing Of Nodule Initiation And Nodule Developmentioning

confidence: 99%

Enhanced nodulation and symbiotic effectiveness of Medicago truncatula when co-inoculated with Pseudomonas fluorescens WSM3457 and Ensifer (Sinorhizobium) medicae WSM419

2011

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Aims Low numbers of rhizobia in soil or inoculants delay nodulation and decrease symbiotic legume productivity. This study investigated the effect of coinoculation with a helper bacterium, Pseudomonas fluorescens WSM3457 on the Medicago truncatulaEnsifer (Sinorhizobium ) medicae WSM419 symbiosis challenged by a low inoculum dose. Methods In a glasshouse experiment the effect of coinoculation with WSM3457 on the kinetics of nodule initiation and development was assessed 5, 7, 10, 14, 17, 21, and 42 days after inoculation of M. truncatula cv. Caliph with 10 3 cells/plant of E. medicae WSM419. Results Co-inoculated plants had enhanced rate of nodule initiation and development, greater numbers of larger crown nodules, and by day 42 accumulated more N than plants inoculated with E. medicae WSM419 alone. Nodule development was altered by co-inoculation. Approximately 25% of nodule initials on co-inoculated plants formed in closely associated pairs, young nodules were larger with multiple meristems and developed into cluster-like multilobed nodules compared to those on WSM419 inoculated plants. Molecular typing showed WSM3457 occupied a significant proportion of root nodules on co-inoculated plants. Conclusion Co-inoculation with P. fluorescens WSM3457 enhanced symbiotic effectiveness of M. truncatula when inoculated with a low inoculum dose of E. medicae WSM419.

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Nocardioides

Evtushenko¹,

Krausova²,

Yoon³

2015

Bergey's Manual of Systematics of Archaea and Bacteria

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No.car.di.o.i'des. N.L. fem. n. Nocardia name of a genus; L. suff. ‐ oides (from Gr. suff. ‐ eides from Gr. n. eidos , that which is seen, form, shape, figure) ressembling, similar; N.L. masc. n. Nocardioides Nocardia ‐like, referring to the similarity of life cycles of the type species of this genus and Nocardia . Actinobacteria / Actinobacteria / Propionibacteriales / Nocardioidaceae / Nocardioides Abundantly branched vegetative hyphae or irregular rods may be formed in young cultures. The morphogenetic cycle is usually observable, with different organisms showing more or less complex succession of morphological stages . The morphogenetic cycle usually starts with the coccoid cells or short rods which may simply germinate into rods or longer filaments, show elementary branching or form extensively branched hyphae on and below the surface of agar media, and may give rise to aerial mycelium . The latter consists of irregular, sparsely branching or unbranched hyphae and may totally or partially cover the primary mycelium, or be discernible only microscopically. Both the vegetative and aerial hyphae and the rod‐shaped cells undergo various degrees of fragmentation (division via septa formation). Fragmentation finally results in the next generation of short rod‐like and coccoid cells. No endospores are formed. Rod‐shaped bacteria may be motile. Gram‐stain‐positive type of cell wall. Non‐acid‐fast. The colony color is mainly whitish, creamy, or yellow of different tint and intensity and rarely orange . Diffusible pigments are not usually produced. Colonies not covered by aerial mycelium are mostly pasty , with smooth to wrinkled surface . Chemo‐organotrophic, with an oxidative type of metabolism. Predominantly catalase‐positive. The level of oxidase activity varies among species. Grows under aerobic conditions on standard laboratory media, including chemically defined (synthetic) media or media with low nutrient concentrations. Certain vitamins or other growth factors may be required. Utilizes a wide range of carbon and nitrogen sources, including unusual organic compounds and toxic environmental pollutants. Mostly mesophilic and neutrophilic; some grow at initial pH values of 5–5.5 and/or 11–12. Mostly non‐halophilic, but salt‐requiring organisms occasionally occur. DNA G + C content ( mol %): 67.5 ( T m )–74.8 (HPLC). Type species : Nocardioides albus Prauser 1976, 61 AL .

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Analysis of a ribosomal RNA operon in the actinomycete Frankia

Cited by 144 publications

References 20 publications

Inter- and Intraspecific Genetic Analysis of the Genus Saccharomonospora with 16S to 23S Ribosomal DNA (rDNA) and 23S to 5S rDNA Internally Transcribed Spacer Sequences

Inter- and Intraspecific Genetic Analysis of the Genus Saccharomonospora with 16S to 23S Ribosomal DNA (rDNA) and 23S to 5S rDNA Internally Transcribed Spacer Sequences

Enhanced nodulation and symbiotic effectiveness of Medicago truncatula when co-inoculated with Pseudomonas fluorescens WSM3457 and Ensifer (Sinorhizobium) medicae WSM419

Nocardioides

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