Two distinct mechanisms cause heterogeneity of 16S rRNA

Abstract

To investigate the frequency of heterogeneity among the multiple 16S rRNA genes within a single microorganism, we determined directly the 120-bp nucleotide sequences containing the hypervariable alpha region of the 16S rRNA gene from 475 Streptomyces strains. Display of the direct sequencing patterns revealed the existence of 136 heterogeneous loci among a total of 33 strains. The heterogeneous loci were detected only in the stem region designated helix 10. All of the substitutions conserved the relevant secondary structure. The 33 strains were divided into two groups: one group, including 22 strains, had less than two heterogeneous bases; the other group, including 11 strains, had five or more heterogeneous bases. The two groups were different in their combinations of heterogeneous bases. The former mainly contained transitional substitutions, and the latter was mainly composed of transversional substitutions, suggesting that at least two mechanisms, possibly misincorporation during DNA replication and horizontal gene transfer, cause rRNA heterogeneity.

FIG. 1

Direct sequencing pattern of the hypervariable α region of S. althioticus JCM4344 16S rDNA. Arrows indicate the loci representing heterogeneity.

FIG. 2

(A) Secondary structures of S. thermodiastaticus JCM4840 16S rRNA regions used this study. Helix numbering is according to the nomenclature (4), and the base position numbering is according to that of S. ambofaciens (18). The arrow indicates the region used as a sequencing primer. Heterogeneous loci are indicated by the abbreviations given in Table 1, footnote a. (B) Secondary structures of helix 10 of two distinct sequences in S. thermodiastaticus 16S rRNAs. Bars and dots indicate Watson-Crick pairing and non-Watson-Crick pairing, respectively.