Retrieval of missing spliced leader in dinoflagellates.

Huan Zhang,Senjie Lin,Christophe Herman

doi:10.1371/journal.pone.0004129

Abstract

Spliced leader (SL) trans-splicing has recently been shown to be a common mRNA processing mechanism in dinoflagellates, in which a short (22-nt) sequence, DCCGUAGCCAUUUUGGCUCAAG (D = U, A, or G), is transplanted from the 5′-end of a small non-coding RNA (SL RNA) to the 5′ end of mRNA molecules. The widespread existence of the mechanism in dinoflagellates has been demonstrated by detection of this SL (DinoSL) in a wide phylogenetic range of dinoflagellates. Furthermore, the presence of DinoSL in the transcripts of highly diverse groups of nuclear-encoded genes has led us to postulate that SL trans-splicing is universal in dinoflagellate nuclear genome. However, some observations inconsistent to this postulation have been reported, exemplified by a recent article reporting apparent absence of DinoSL in the transcripts of some nuclear-encoded genes in Amphidinium carterae. Absence of SL in these gene transcripts would have important implication on gene regulation in dinoflagellates and utility of DinoSL as a universal dinoflagellate-specific primer to study dinoflagellate transcriptomics. In this study, we re-examined transcripts of these genes and found that all of them actually contained DinoSL. Therefore, results to date are consistent to our initial postulation that DinoSL occurs in all dinoflagellate nuclear-encoded mRNAs.

Highlights

To the list of unusual molecular and cytological characteristics of dinoflagellate recognized in the last two decades was recently added another: these organisms possess a unique spliced leader (SL) trans-splicing machinery [1,2]
Wide cDNA size range in the Spliced leader (SL)-based full-length cDNA libraries for Amphidinium carterae and Karlodinium veneficum
To address whether detection of this SL (DinoSL) only occurs in a selection of cDNAs, we ran a subsample of the full-length cDNA libraries on the agarose gel to examine whether the libraries were biased toward certain molecular weight range or discrete molecular size bands

Summary

Introduction

To the list of unusual molecular and cytological characteristics of dinoflagellate recognized in the last two decades was recently added another: these organisms possess a unique spliced leader (SL) trans-splicing machinery [1,2]. While the conserved Sm-binding site [Sm motif] in other organisms (RAU4-6GR in the kinetoplastids, freshwater planarians and Caenorhabditis, RAUUUUCGG in Hydra, AGCUUUGG in Ciona, AGCUUUUCUUUGG in Schistosoma, and AAYUYUGA in Rotifera ([1] and refs there in) usually is located in the intron of the SL RNA, dinoflagellate SL intron does not carry this Smbinding site; instead a sequence (AUUUUGG) highly similar to the binding site exists in the exon This observation suggests that either dinoflagellates use a unique Sm-binding site located in the intron, or the apparent Sm-binding site in the exon functions in trans-splicing. The proposition that SL RNA in K. brevis and probably other dinoflagellates contains a longer intron that possesses a Sm-binding site is not supported

Methods

Results

Conclusion