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...

We describe here the presence of two distinct types of rRNA operons in the genome of a thermophilic actinomycete Thermomonospora chromogena. The genome of T. chromogena contains six rRNA operons (rrn), of which four complete and two incomplete ones were cloned and sequenced. Comparative analysis revealed that the operon rrnB exhibits high levels of sequence variations to the other five nearly identical ones throughout the entire length of the operon. The coding sequences for the 16S and 23S rRNA genes differ by approximately 6 and 10%, respectively, between the two types of operons. Normal functionality ofrrnB is concluded on the basis of the nonrandom distribution of nucleotide substitutions, the presence of compensating nucleotide covariations, the preservation of secondary and tertiary rRNA structures, and the detection of correctly processed rRNAs in the cell. Comparative sequence analysis also revealed a close evolutionary relationship between rrnB operon of T. chromogena and rrnA operon of another thermophilic actinomycete Thermobispora bispora. We propose thatT. chromogena acquired rrnB operon fromT. bispora or a related organism via horizontal gene transfer.

rRNA genes are thought unlikely to be laterally transferred, because rRNA must coevolve with a large number of cellular components to form the highly sophisticated translation apparatus and perform protein synthesis. In this paper, the authors first hypothesized that lateral gene transfer (LGT) might occur to rRNA genes via replacement of gene segments encoding individual domains of rRNA : the ' simplified complexity hypothesis '. Comparative sequence analyses of the 16S and 23S rRNA genes from a large number of actinomycete species frequently identified rRNA genes containing short segments with an abnormally high number of non-random base variations. These variations were nearly always characterized by complementing covariations of several paired bases within the stem of a hairpin. The nature of these base variations is not consistent with random mutations but satisfies well the predictions of the ' simplified complexity hypothesis '. The most parsimonious explanation for this phenomenon is the lateral transfer of rRNA gene segments between different bacterial species. This mode of LGT may create mosaic rRNA genes and occur repeatedly in different regions of a gene, gradually destroying the evolutionary history recorded in the nucleotide sequence.