Group II introns are genetic retroelements capable of selfsplicing and mobility that are widespread in prokaryotes. Originally discovered in organelles of fungi, plants, and lower eukaryotes ϳ20 years ago (33), they were first found in bacteria ϳ10 years later (15) and lately have been identified in archaea of the Methanosarcina genus (11, 55). About 25% of the completely sequenced microbial genomes, covering a diverse range of bacterial phyla, contain one or more introns (either full length or fragmented). A compilation of bacterial group II introns showed that these elements are often inserted in intergenic regions, and when located inside genes, they are rarely found within highly conserved or housekeeping genes (10). Usually, bacterial group II introns are located on mobile DNA elements such as plasmids, insertion elements, transposons, or pathogenicity islands, which could account for their spread among bacteria (4, 10).Group II introns typically consist of a catalytic RNA containing an internal protein-encoding open reading frame (ORF), although many ORF-less introns exist in eukaryotic organelles. Functional introns are able to excise out of RNA transcripts (self-splicing), and insert (reverse splice) into identical intronless DNA sites (process called homing) or into novel (ectopic) genomic locations but at a much lower frequency (retrotransposition). The homing process is highly site specific and occurs at target regions spanning ϳ30 bp around the insertion point (18, 51). Selection of splice sites is determined by base pairings between three motifs in the intron RNA (exon-binding sequences EBS1, EBS2, and EBS3 or ␦) and the complementary sequences in the flanking exons (intron-binding sequences IBS1, IBS2, and IBS3 or ␦Ј, respectively), and these pairings are required for both splicing and reverse splicing (insertion). The splicing reactions are intrinsically catalyzed by the RNA part, but the intronic protein participates in vivo in both the splicing and insertion events (see references 5 and 55 for reviews). Because of the similar in vitro splicing mechanism, including formation of a lariat structure, group II introns are thought to be the ancestors of the nuclear spliceosomal introns of eukaryotes. The secondary structure of the group II RNA is made up of six domains linked by tertiary interactions, where domain V is the presumed catalytic core and domain VI contains a bulged A that is the branching point of the lariat (34,35,42,54). The structure is used to divide the group II introns into subclasses (54). The intron-encoded protein (IEP), located in domain IV, is a multifunctional protein that can have three functional domains: a reverse transcriptase (RT) domain for synthesis of DNA strand upon insertion, a maturase (X) domain involved in splicing, and an endonuclease (En or Zn) domain for target DNA cleavage, although the latter region is lacking in most IEPs. In between the X and En domains is a DNA-binding (D) region (3,5,50,57).For many published bacterial genome sequences, the IEPs are annot...

No abstract

The Bacillus cereus group of bacteria is a group of closely related species that are of medical and economic relevance, including B. anthracis, B. cereus, and B. thuringiensis. Bacteria from the Bacillus cereus group encode three large, highly conserved genes of unknown function (named crdA, crdB, and crdC) that are composed of 16 to 35 copies of a repeated domain of 132 amino acids at the protein level. Bioinformatic analysis revealed that there is a phylogenetic bias in the genomic distribution of these genes and that strains harboring all three large genes mainly belong to cluster III of the B. cereus group phylogenetic tree. The evolutionary history of the three large genes implicates gain, loss, duplication, internal deletion, and lateral transfer. Furthermore, we show that the transcription of previously identified antisense open reading frames in crdB is simultaneously regulated with its host gene throughout the life cycle in vitro, with the highest expression being at the onset of sporulation. In B. anthracis, different combinations of double-and triple-knockout mutants of the three large genes displayed slower and less efficient sporulation processes than the parental strain. Altogether, the functional studies suggest an involvement of these three large genes in the sporulation process.