Euglena Transcript Processing

Abstract

RNA transcript processing is an important stage in the gene expression pathway of all organisms and is subject to various mechanisms of control that influence the final levels of gene products. RNA processing involves events such as nuclease-mediated cleavage, removal of intervening sequences referred to as introns and modifications to RNA structure (nucleoside modification and editing). In Euglena, RNA transcript processing was initially examined in chloroplasts because of historical interest in the secondary endosymbiotic origin of this organelle in this organism. More recent efforts to examine mitochondrial genome structure and RNA maturation have been stimulated by the discovery of unusual processing pathways in other Euglenozoans such as kinetoplastids and diplonemids. Eukaryotes containing large genomes are now known to typically contain large collections of introns and regulatory RNAs involved in RNA processing events, and Euglena gracilis in particular has a relatively large genome for a protist. Studies examining the structure of nuclear genes and the mechanisms involved in nuclear RNA processing have revealed that indeed Euglena contains large numbers of introns in the limited set of genes so far examined and also possesses large numbers of specific classes of regulatory and processing RNAs, such as small nucleolar RNAs (snoRNAs). Most interestingly, these studies have also revealed that Euglena possesses novel processing pathways generating highly fragmented cytosolic ribosomal RNAs and subunits and non-conventional intron classes removed by unknown splicing mechanisms. This unexpected diversity in RNA processing pathways emphasizes the importance of identifying the components involved in these processing mechanisms and their evolutionary emergence in Euglena species.

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

“…Although only a small number of euglenid genes and their corresponding mRNAs have been sequenced and annotated, three types of cis-spliced introns have been found (McWatters & Russell, 2017). Conventional spliceosomal introns with 5 -GT/AG-3 borders have been found in the euglenid tubulin genes (Ebel et al, 1999;Canaday et al, 2001 ;Milanowski et al, 2014Milanowski et al, , 2016Ebenezer et al, 2017), fibrillarin gene (Breckenridge et al, 1999;Russell et al, 2005), a GapC gene (encoding cytosolic glyceraldehyde-3-phosphate dehydrogenase) (Milanowski et al, 2016) and in the second half of the presequence-encoding regions or slightly downstream from this region in eight nucleus-encoded E. gracilis genes for chloroplast proteins -enolase (Eno29), porphobilinogen deaminase (Pbgd), glyceraldehyde-3-phosphate dehydrogenase (GapA), cytochrome f (PetA), ferredoxin (PetF), subunit F of photosystem I (PsaF), and subunits M and W of photosystem II (PsbM and PsbW) (Vesteg et al, 2010).…”

“…Non-conventional introns are also found in the tubulin genes (Canaday et al, 2001;Milanowski et al, 2014Milanowski et al, , 2016Ebenezer et al, 2017) and Hsp90 (encoding heat shock protein 90) genes (Breglia, Slamovits & Leander, 2007;Milanowski et al, 2016) of a number of euglenids indicating that they are not restricted to genes encoding chloroplast-localized proteins. Non-conventional introns do not have the conserved 5 -GT/AG-3 splicing borders, the 5 -end is not complementary to the U1 snRNA indicating that spliceosomes are probably not involved in their excision, they lack the structural characteristics of group I and II introns, many are flanked by short direct repeats confounding identification of the splice sites and they can form secondary structures which could potentially bring together the 5 and 3 intron ends (Muchhal & Schwartzbach, 1992Henze et al, 1995;Tessier et al, 1995;Canaday et al, 2001;Breglia et al, 2007;Milanowski et al, 2014Milanowski et al, , 2016Ebenezer et al, 2017;McWatters & Russell, 2017).…”

“…Both non-conventional and conventional introns are found in some euglenid genes (Breglia et al, 2007;Milanowski et al, 2014Milanowski et al, , 2016Ebenezer et al, 2017Ebenezer et al, , 2019McWatters & Russell, 2017). In 20 species of euglenids, the positions of the conventional spliceosomal introns in the TubA and TubB 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, 2014).…”

“…The intermediate introns are considered by some to be a third type of intron present in euglenids (Canaday et al, 2001;Russell et al, 2005;Milanowski et al, 2014Milanowski et al, , 2016Ebenezer et al, 2017Ebenezer et al, , 2019McWatters & Russell, 2017). The intermediate introns have features of both conventional and non-conventional introns.…”

RNA-Seq employing a novel rRNA depletion strategy reveals a rich repertoire of snoRNAs in Euglena gracilis including box C/D and Ψ-guide RNAs targeting the modification of rRNA extremities

“…E. gracilis is a particularly interesting organism in which to characterize ncRNAs because of the many unusual features of its cellular biology and gene expression strategies that suggest it may contain a large collection of ncRNAs [7,8]. Recently, mRNA transcriptome studies have been performed [9,10] that indicate that E. gracilis has extensive protein-coding potential and it has been suggested that expression of nuclear proteincoding genes is extensively controlled at the post-transcriptional level.…”