Distribution of Conventional and Nonconventional Introns in Tubulin (α and β) Genes of Euglenids

Abstract

The nuclear genomes of euglenids contain three types of introns: conventional spliceosomal introns, nonconventional introns for which a splicing mechanism is unknown (variable noncanonical borders, RNA secondary structure bringing together intron ends), and so-called intermediate introns, which combine features of conventional and nonconventional introns. Analysis of two genes, tubA and tubB, from 20 species of euglenids reveals contrasting distribution patterns of conventional and nonconventional introns—positions of conventional introns are conserved, whereas those of the nonconventional ones are unique to individual species or small groups of closely related taxa. Moreover, in the group of phototrophic euglenids, 11 events of conventional intron loss versus 15 events of nonconventional intron gain were identified. A comparison of all nonconventional intron sequences highlighted the most conserved elements in their sequence and secondary structure. Our results led us to put forward two hypotheses. 1) The first one posits that mutational changes in intron sequence could lead to a change in their excision mechanism—intermediate introns would then be a transitional form between the conventional and nonconventional introns. 2) The second hypothesis concerns the origin of nonconventional introns—because of the presence of inverted repeats near their ends, insertion of MITE-like transposon elements is proposed as a possible source of new introns.

Euglena gracilis Genome and Transcriptome: Organelles, Nuclear Genome Assembly Strategies and Initial Features

“…7.5) (for details on Euglenoid introns see Milanowski et al 2014, 2016, andMcWaters andRussell, this volume). Overall gene lengths in the transcriptome are similar to those previously reported (Schantz and Schantz 1989;Jackson et al 2006;Levasseur et al 1994;Milanowski et al 2014Milanowski et al , 2016Canaday et al 2001), but are considerably shorter in the genome owing to truncation and fragmentation.…”

Euglena Transcript Processing

“…These could potentially be excised using components of both the spliceosome and trans-acting non-conventional intron splicing factors. Milanowski et al have recently examined the conservation of intron position and class in conserved nuclear genes in different Euglena species to shed light on such questions (Milanowski et al 2014(Milanowski et al , 2016. These studies have further refined the limited conserved sequence and structural features of non-conventional introns (as described above) and revealed that non-conventional intron gain/loss appears to occur much more frequently than observed for euglenid spliceosomal introns.…”

“…The non-conventional introns are defined as containing extensive secondary structural potential via base-pairing of intron 5′ and 3′ end proximal sequences, but little overall intron sequence conservation (Tessier et al 1991;Canaday et al 2001;Russell et al 2005;Milanowski et al 2014Milanowski et al , 2016Schwartzbach 1992, 1994) (Fig. 8.1b).…”

“…The lack of strict conservation of the direct repeats and their sequence variability indicates that they are unlikely to have a role in the splicing mechanism but may instead be remnants of intron sequence insertion and mobility events. Milanowski et al have noted that these features are reminiscent of MITE-like transposon elements (Milanowski et al 2014); therefore, if the non-conventional introns have been derived from such elements then perhaps trans-acting factors that associate with them may have been co-opted to be involved in the splicing mechanism. While there is no apparent conservation of extended sequence elements in these introns, intron sequence comparisons have revealed a preference for intron 5′ end proximal nucleotide positions +4 to +6 to be 'CAG' and the complementary sequence (CTG) starting 6 nucleotides from the intron 3′ end (Milanowski et al 2014(Milanowski et al , 2016 (Fig.…”

“…Some of the Euglena non-conventional introns contain intron terminal nucleotides (5′GT or AG3′) identical to those of most conventional spliceosomal introns (Canaday et al 2001;Milanowski et al 2014) (Fig. 8.1a).…”