Order of removal of conventional and nonconventional introns from nuclear transcripts of Euglena gracilis

Abstract

Nuclear genes of euglenids and marine diplonemids harbor atypical, nonconventional introns which are not observed in the genomes of other eukaryotes. Nonconventional introns do not have the conserved borders characteristic for spliceosomal introns or the sequence complementary to U1 snRNA at the 5' end. They form a stable secondary structure bringing together both exon/intron junctions, nevertheless, this conformation does not resemble the form of self-splicing or tRNA introns. In the genes studied so far, frequent nonconventional introns insertions at new positions have been observed, whereas conventional introns have been either found at the conserved positions, or simply lost. In this work, we examined the order of intron removal from Euglena gracilis transcripts of the tubA and gapC genes, which contain two types of introns: nonconventional and spliceosomal. The relative order of intron excision was compared for pairs of introns belonging to different types. Furthermore, intermediate products of splicing were analyzed using the PacBio Next Generation Sequencing system. The analysis led to the main conclusion that nonconventional introns are removed in a rapid way but later than spliceosomal introns. Moreover, the observed accumulation of transcripts with conventional introns removed and nonconventional present may suggest the existence of a time gap between the two types of splicing.

Metabolic quirks and the colourful history of the Euglena gracilis secondary plastid

“…The ultrastructure, metabolism, plastid and mitochondrial genomes of E. gracilis have been studied in great detail (Tessier et al, 1991;Hallick et al, 1993;Muchhal & Schwartzbach, 1994;Jenkins et al, 1995;Doetsch et al, 2001;Geimer et al, 2009; Mate a sikov a-Kov a cov a et al, 2012; Kuo et al, 2013;Dob akov a et al, 2015;Watanabe et al, 2017;Gumi nska et al, 2018). Moreover, three transcriptome datasets have been generated recently (O'Neill et al, 2015;Yoshida et al, 2016;Ebenezer et al, 2019), the last coupled with a draft genome and proteomics analysis of whole-cell lysates.…”

Heterotrophic Euglenid Rhabdomonas Costata Resembles Its Phototrophic Relatives in Many Aspects of Molecular and Cell Biology

“…Conversely, the quality of the transcriptome dataset was sufficient for functional annotation. The number of non-redundant predicted proteins (39,585) is comparable to E. gracilis (36,526) 13 . Mature euglenid transcripts often contain splice leader (SL) sequences acquired by trans-splicing 19 .…”

“…However, the genes of euglenids also contain also nonconventional introns variable in length and with no clear pattern of the nucleotide sequence at the exon/intron junction. They form the stem-loop RNA structures, and their excision is probably independent of the spliceosome, taking place after the excision of spliceosomal introns 20,36 . Besides these main types of introns, so-called intermediate introns that combine the features of both types have been reported 20 .…”

Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa

“…In 20 species of euglenids, the positions of the conventional spliceosomal introns in the Tub A and Tub B genes (encoding α‐ and β‐tubulin, respectively) are conserved, while the positions of the non‐conventional introns are lineage or species specific (Milanowski et al, ). The conventional introns appear to be removed prior to removal of the non‐conventional introns (Gumińska et al, ). Non‐conventional intron formation appears to be an ongoing process as evidenced by the recently acquired non‐conventional intron in the Gap C gene of Euglena agilis (Milanowski et al, ).…”