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Intragenomic and intraspecific polymorphism of the 16S–23S rDNA internally transcribed sequences of Streptomyces ambofaciens

Laboratoire de Génétique et Microbiologie UMR INRA 1128-IFR110, Faculté des Sciences, Université Henri Poincaré – Nancy 1, BP 239, Boulevard des Aiguillettes, F-54506 Vandoeuvre-lès-Nancy, France¹

Author for correspondence: Pierre Leblond. Tel: +33 03 83 91 22 04. Fax: +33 03 83 91 25 00. e-mail: leblond{at}nancy.inra.fr

The nucleotide composition of the internally transcribed sequences (ITSs) of the six rDNA operons of two strains of Streptomyces ambofaciens were determined. Four variable and five conserved nucleotide blocks were distinguished. Five different modular organizations were revealed for each strain and no homologous loci showed the same succession of blocks. This suggests that recombination frequently occurs between the rDNA loci, leading to the exchange of nucleotide blocks. The modular structure was also observed within the ITSs of Streptomyces coelicolor M145, which is closely related to Streptomyces ambofaciens, and Streptomyces griseus 2247, showing the same number of constant blocks but with fewer variable regions. This confirms that a high degree of ITS variability is a common characteristic among Streptomyces spp. The functional significance of the combinations of variable and constant nucleotide blocks of the ITS was examined by in silico prediction of secondary structures from nucleotide sequences. The secondary structures were shown to be analogous whatever the combination of variable/constant blocks at the intragenomic, intraspecific and interspecific levels.

Keywords: rDNA evolution, gene conversion, recombination, intergenic spacer, ITS

Abbreviations: ATCC, American Type Culture Collection; DSM, Deutsche Sammlung von Mikroorganismen und Zelkulturen; dsPS, double-stranded processing site; ITS, internally transcribed sequence; c, constant region; v, variable region; vc, variable/constant region

The GenBank accession numbers for the sequences reported in this paper can be found in Table 1.

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