Group I introns are mobile genetic elements that have not previously been found in bacterial ribosomal DNA (rDNA), despite the fact that nearly all bacterial 23S rDNAs have conserved target sequences for the intron-encoded homing endonucleases I-Ceu
) and I-Cpa
). Upon intron entry into cells, homing endonucleases are expressed and mediate intron insertion into host DNA by cleaving intronless target sites (5
). Group I 23S rDNA introns are widespread in algal chloroplasts (49
), which are thought to be derived from bacterial ancestors (21
). The 23S rDNA group I introns are also found in the apparently bacterially derived mitochondria (32
) of an amoeba and other lower eukaryotes (22
). They are present in the nuclear rDNA of lower eukaryotes and archaea (22
). It is not known why bacteria lack rDNA introns.
Some bacterial ribosomal genes encode intervening segments (IVSs) that are approximately the size of small introns. These are excised from the rRNA by ribonucleases, leaving fragmented but functional rRNA. IVSs are found in highly variable regions, not in functionally essential domains (23
). In contrast, group I introns are located in functionally vital loci and must be removed from transcripts by autocatalytic splicing or by splicing that is facilitated by maturase protein (7
). Splicing occurs coordinately with ligation of the RNA exons (12
). The intron transcript folds to form a catalytic core for carrying out the splicing and ligation. The core structure can be predicted by RNA folding analysis (24
), and 10 complementary domains with specific roles in core formation, P1 to P10, have been deduced by sequence similarity, covariance of distant positions, and stereochemical modeling (39
). Neither sequence nor folding analysis, however, predicts whether group I splicing will be autocatalytic or maturase facilitated. Autocatalysis can be tested by an in vitro assay (26
). Maturases must be encoded by the introns themselves or supplied endogenously or exogenously.
Although the 16S small ribosomal subunit (SSU) genes of species belonging to the bacterial order Chlamydiales
are well characterized, chlamydial 23S rRNA large ribosomal subunit (LSU) genes have undergone only partial and limited scrutiny (17
). Chlamydiae are obligately intracellular bacteria that replicate only within endocytic vacuoles of eukaryotic cells. Four families of chlamydiae are known to parasitize vertebrates or have been associated with vertebrates (8
), and those strains belonging to Parachlamydia acanthamoebae
also live in amoebae (2
). In a comprehensive analysis of chlamydial 23S rRNA, a group I intron was identified in Simkania negevensis
, a Chlamydiales
strain for which the natural eukaryotic host is not known. This is the first bacterium that has been found to have a 23S rRNA group I intron. The intron is characterized in this study.