Abstract
Group II introns are ribozymes and retroelements found in bacteria, and are thought to have been the ancestors of nuclear pre-mRNA introns. Whereas nuclear introns undergo prolific alternative splicing in some species, group II introns are not known to carry out equivalent reactions. Here we report a group II intron in the human pathogen Clostridium tetani, which undergoes four alternative splicing reactions in vivo. Together with unspliced transcript, five mRNAs are produced, each encoding a distinct surface layer protein isoform. Correct fusion of exon reading frames requires a shifted 5′ splice site located 8 nt upstream of the canonical boundary motif. The shifted junction is accomplished by an altered IBS1-EBS1 pairing between the intron and 5′ exon. Growth of C. tetani under a variety of conditions did not result in large changes in alternative splicing levels, raising the possibility that alternative splicing is constitutive. This work demonstrates a novel type of gene organization and regulation in bacteria, and provides an additional parallel between group II and nuclear pre-mRNA introns.
Highlights
Group II introns are large catalytic RNAs and retroelements found within prokaryotic genomes, as well as in organellar genomes of eukaryotes such as fungi, plants and protists [1,2,3]
During a bioinformatic search for open reading frame (ORF)-less group II introns in bacterial genomes [17], a novel intron-related sequence was identified in the genome of C. tetani E88
Within a 5.1 kb region, four intron domain 5 (D5) motifs were detected, each of nearly identical sequence, and each followed by a domain 6 (D6) motif (Figure 1)
Summary
Group II introns are large catalytic RNAs and retroelements found within prokaryotic genomes, as well as in organellar genomes of eukaryotes such as fungi, plants and protists [1,2,3]. Despite the self-splicing capability of group II introns, splicing in vivo requires the IEP to stabilize the catalytically active RNA structure. The IEP functions in the integration of the intron sequence into new genomic locations through well-studied retrohoming and retrotransposition mechanisms [12,13,14,15]. This mobile form of group II introns, consisting of both ribozyme and RT-related IEP, predominates in bacteria and is considered the ancestral form of extant group II introns [16,17]
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