Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer

Abstract

Paulinella micropora is a rhizarian thecate amoeba, belonging to a photosynthetic Paulinella species group that has a unique organelle termed chromatophore, whose cyanobacterial origin is distinct from that of plant and algal chloroplasts. Because acquisition of the chromatophore was quite a recent event compared with that of the chloroplast ancestor, the Paulinella species are thought to be model organisms for studying the early process of primary endosymbiosis. To obtain insight into how endosymbiotically transferred genes acquire expression competence in the host nucleus, here we analyzed the 5′ end sequences of the mRNAs of P. micropora MYN1 strain with the aid of a cap-trapper cDNA library. As a result, we found that mRNAs of 27 genes, including endosymbiotically transferred genes, possessed the common 5′ end sequence of 28–33 bases that were posttranscriptionally added by spliced leader (SL) trans-splicing. We also found two subtypes of SL RNA genes encoded by the P. micropora MYN1 genome. Differing from the other SL trans-splicing organisms that usually possess poly(A)-less SL RNAs, this amoeba has polyadenylated SL RNAs. In this study, we characterize the SL trans-splicing of this unique organism and discuss the putative merits of SL trans-splicing in functional gene transfer and genome evolution.

SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data

“…Most RNA-Seq library preparation methods also show considerable loss of coverage at the 5′ end, which often limits SL detection to a short c. 10 bp portion at typically < 1% of reads [20,36,66]. This means that SLOPPR in particular is likely to underestimate the extent of SL trans-splicing and operonic gene organisation unless huge amounts of sequencing data are available [35] or specialised SL-enrichment library preparation methods are used [19,23,30]. However, our SLIDR analysis on Hydra vulgaris vividly demonstrates that SLs at nearly 100% of all genes can be detected from RNA-Seq data if coverage is sufficient.…”

SLIDR and SLOPPR: Flexible identification of spliced leadertrans-splicing and prediction of eukaryotic operons from RNA-Seq data

“…Most RNA-Seq library preparation methods also show considerable loss of coverage at the 5' end, which often limits SL detection to a short c. 10 bp portion at typically <1 % of reads [19,35,73]. This means that SLOPPR in particular is likely to underestimate the extent of SL trans-splicing and operonic gene organisation unless huge amounts of sequencing data are available [34] or specialised SL-enrichment library preparation methods are used [18,22,29]. However, our SLIDR analysis on Hydra vulgaris vividly demonstrates that SLs at nearly 100 % of all genes can be detected from RNA-Seq data if coverage is sufficient.…”

SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

“…[ 2 ]). SL transcript sequences can be divided into two regions: an exon like sequence that remains in the final trans-spliced transcript and an intron that usually contains a canonical Sm-protein-binding site (see for exceptions: [ 3 , 4 ]), separated by a splice donor site [ 1 ].…”

“…So far SL Trans-Splicing has been reported in groups such as Euglenozoa [15,16], Platyhelminthes [17,18], Nematoda [19,20], Urochordata [21], Rotifera [22], Cnidaria [23], Dinoflagellata [24], Crustaceans [25] and Amoebozoa [4]. However, it is absent in others such as vertebrates, insects, plants, Fungi and several protists [14,26].…”