Designation of Streptomycete 16S and 23S rRNA-based target regions for oligonucleotide probes

Abstract

The 16S and 23S rRNA of various Streptomyces species were partially sequenced and screened for the presence of stretches that could define all members of the genus, groups of species, or individual species. Nucleotide 929 (Streptomyces ambofaciens nomenclature [J. L. Pernodet, M. T. Alegre, F. Boccard, and M. Guerineau, Gene 79:33-46, 19891) is a nucleotide highly unique to Streptomyces species which, in combination with flanking regions, allowed the designation of a genus-specific probe. Regions 158 through 203 of the 16S rRNA and 1518 through 1645 of the 23S rRNA (helix 54 [Pernodet et al., Gene 79:33-46, 1989]) have a high potential to define species, whereas the degree of variation in regions 982 through 998 and 1102 through 1122 of the 16S rRNA is less pronounced but characteristic for at least certain species. Alone or in combination with each other, these regions may serve as target sites for synthetic oligonucleotide probes and primers to be used in the determination of pure cultures and in the characterization of community structures. The specificity of several probes is demonstrated by dot blot hybridization.

Effects of plant host species and plant community richness on streptomycete community structure

“…We used StrepB (Rintala et al, 2001) as our forward primer, and the reverse complement of Act283 (McVeigh et al, 1996) as our reverse primer, each at a final concentration of 200 nM. Both primers are selective and together amplify a fragment of approximately 165 nucleotides, encompassing the V2 variable region of the 16S rRNA gene, which is referred to as the 'gamma variable region' in older studies of streptomycetes (Stackebrandt et al, 1991). Primers were modified to contain one of 30 different 10mer identifying barcodes (Parameswaran et al, 2007).…”

Phenotypic, genotypic and pathogenic variation among streptomycetes implicated in common scab disease

“…Unalignable regions, regions with gaps, or regions lacking sequence for all strains were removed prior to phylogenetic analyses which were conducted with approximately 300 bp. The region of 16S rRNA used for this analysis includes the hypervariable g-region (Stackebrandt et al 1991). Neighbour-joining was used for the reconstruction of phylogenetic relationships (PHYLIP; Felsenstein 1993) with Escherichia coli used as the outgroup.…”

Two Distinct Mechanisms Cause Heterogeneity of 16S rRNA

“…In virtually all species, the sequences of multicopy rRNA genes are identical or nearly identical and the homogeneity is thought to be governed by concerted evolution (8), which may originate from stringent selective pressure on the primary sequences of rRNA molecules to maintain their precise interactions with components of the complex protein-synthesizing machinery (29). From these characteristics, the DNA sequences of the 16S rRNA genes (rDNA) have become powerful tools in modern prokaryotic taxonomy with the increasing use of PCR technology (21,25,26).…”