The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes

Abstract

Here we present the first description of the presence of two distinct types of 16S rRNA genes in the genome of a (eu)bacterium, Thermobispora bispora. We cloned and determined the nucleotide sequences of all four rRNA operons of T. bispora. Sequence comparisons revealed that the genome of T. bispora contains two distinct types of 16S rRNA genes, each type consisting of two identical or nearly identical copies, and three identical copies of the 23S RNA gene. The nucleotide sequences of the two types of 16S rRNA genes differ at 98 nucleotide positions (6.4% of total nucleotides) together with six regions of deletion-insertions. None of the base substitutions or insertion-deletions corresponds to any of the approximately 600 evolutionarily invariable or rarely variable nucleotides, indicating that both genes are functional. Both types of 16S rRNA genes are transcribed and processed as determined by Northern (RNA) hybridization and reverse transcriptase-mediated PCR.Most organisms have multiple copies of rRNA genes. It is generally believed that all the copies of rRNA genes of an organism are identical or nearly identical in nucleotide sequence (18, 37). The homogeneity of rRNA genes is thought to occur by concerted evolution (13) of the repeated genes and stringent selection pressure on the primary sequences of rRNA molecules to maintain their precise interactions with components of the complex protein-synthesizing machinery (37). For the same reason, rRNA genes are thought unlikely to be horizontally transferred between organisms. The homogeneity of rRNA genes, together with some other properties, makes them the most widely used molecular chronometers for inferring phylogenetic relationships between organisms (1, 16, 37, 38.) However, several recent reports described considerable differences in nucleotide sequences between copies of rRNA genes in a single organism. The first reports came from the studies of 5S rRNA genes of the amphibian Xenopus laevis (33) and the loach Misgurnus fossilis (21). Both organisms have two classes of 5S rRNAs that are specific to either somatic or oocyte ribosomes. The genome of the eucaryotic parasite Plasmodium berghei contains two types of 18S rRNA genes which differ at 3.5% of the nucleotide positions and demonstrate life cycle stage-specific expression (11,23,32), and the metazoan Dugesia mediterranea possesses two types of 18S rRNA genes with 8% dissimilarity (5). An archaebacterium, Haloarcula marismortui (24, 25), was also reported to contain two distinct types of transcriptionally active 16S RNA genes. Although the number of such cases is small, they may represent a fairly common phenomenon considering the limited number of cases in which nucleotide sequences are available for all copies of an rRNA gene of an organism. Thus, the possession of different types of an rRNA gene in an organism may serve some unknown but essential biological functions.In a previous study of the phylogenetic position of the actinomycete Thermobispora bispora (31), we obtained complete nucleotide seq...

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