Database for bacterial group II introns

Abstract

The Database for Bacterial Group II Introns (http://webapps2.ucalgary.ca/~groupii/index.html#) provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. The website is divided into three sections. The first section provides general information on group II intron properties, structures and classification. The second and main section lists information for individual introns, including insertion sites, DNA sequences, intron-encoded protein sequences and RNA secondary structure models. The final section provides tools for identification and analysis of intron sequences. These include a step-by-step guide to identify introns in genomic sequences, a local BLAST tool to identify closest intron relatives to a query sequence, and a boundary-finding tool that predicts 5′ and 3′ intron–exon junctions in an input DNA sequence. Finally, selected intron data can be downloaded in FASTA format. It is hoped that this database will be a useful resource not only to group II intron and RNA researchers, but also to microbiologists who encounter these unexpected introns in genomic sequences.

NMR structure of the 5′ splice site in the group IIB intron Sc.ai5γ—conformational requirements for exon–intron recognition

“…The particular geometry of the splice site and its orientation with respect to the stem is the result of the interplay between the steric demands of the EBS1•IBS1 helix itself and of the interactions of the four asymmetrically distributed loop nucleotides before and after EBS1. In the light of these findings, it is interesting to compare how many nucleotides precede and follow EBS1 in the different structural subdivisions of group IIB introns and introns with B-like hybrid structures (see the group II intron data base; http://www.fp.ucalgary.ca/group2introns/) (Dai et al 2003;Candales et al 2012). Indeed, it seems that in order to accommodate and orient the EBS1•IBS1 helix and the δ-δ ′ base pair (Fig.…”

RNA–RNA interactions and pre-mRNA mislocalization as drivers of group II intron loss from nuclear genomes

“…intron-mediated nuclear gene silencing | spliceosomal intron evolution G roup II introns that reside in genomes of bacteria, archaea, and eukaryotic organelles are ribozymes that self-splice from pre-mRNA transcripts independent of protein catalysis (1)(2)(3). Group II introns are also mobile retroelements that integrate into DNAs via an RNA intermediate (2,3).…”

“…It is widely speculated that group II introns entered the eukaryotic lineage with the mitochondrial endosymbiosis, invaded the nucleus, and evolved from RNA catalysts into efficient spliceosomedependent introns. However, group II introns are strikingly absent from modern nuclear genomes (1), which are replete with spliceosomal introns. It is still elusive how the ancestral group II introns might have evolved into spliceosomal introns or how they were expunged from nuclear genomes.…”

Novel RNA structural features of an alternatively splicing group II intron from Clostridium tetani

“…1) is a IIB structure belonging to Class B (McNeil et al 2014). This was initially observed based on the closest intron relatives using a local BLASTN database search tool (Candales et al 2012; http:// webapps2.ucalgary.ca/~groupii/index.html#), in which the five introns most closely related to C.te.I1 all belonged to Class B. Consistent with the classification, the C.te.I1 secondary structure has features shared by essentially all Class B introns (Fig.…”