Transcriptome, proteome and draft genome of Euglena gracilis

Abstract

BackgroundPhotosynthetic euglenids are major contributors to fresh water ecosystems. Euglena gracilis in particular has noted metabolic flexibility, reflected by an ability to thrive in a range of harsh environments. E. gracilis has been a popular model organism and of considerable biotechnological interest, but the absence of a gene catalogue has hampered both basic research and translational efforts.ResultsWe report a detailed transcriptome and partial genome for E. gracilis Z1. The nuclear genome is estimated to be around 500 Mb in size, and the transcriptome encodes over 36,000 proteins and the genome possesses less than 1% coding sequence. Annotation of coding sequences indicates a highly sophisticated endomembrane system, RNA processing mechanisms and nuclear genome contributions from several photosynthetic lineages. Multiple gene families, including likely signal transduction components, have been massively expanded. Alterations in protein abundance are controlled post-transcriptionally between light and dark conditions, surprisingly similar to trypanosomatids.ConclusionsOur data provide evidence that a range of photosynthetic eukaryotes contributed to the Euglena nuclear genome, evidence in support of the ‘shopping bag’ hypothesis for plastid acquisition. We also suggest that euglenids possess unique regulatory mechanisms for achieving extreme adaptability, through mechanisms of paralog expansion and gene acquisition.Electronic supplementary materialThe online version of this article (10.1186/s12915-019-0626-8) contains supplementary material, which is available to authorized users.

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

“…A direct BLAST search of the whole transcriptome confirmed that the enzymes of amino acid biosynthesis are indeed present (E. gracilis does not require supplementation by any amino acid when grown autotrophically on minimal medium; Hall & Schoenborn, 1939), but their localisation is nonplastidial, in agreement with the previous in silico prediction (Ebenezer et al, 2019). Only an incomplete serine synthesis pathway was reconstructed, with no identifiable plastidtargeted phosphoserine aminotransferase.…”

“…We also identified 74/83 (89%) and 113/ 131 (86%) high-confidence plastid-targeted candidates from two earlier studies (Durnford & Gray, 2006; Z ahonov a et al, 2018; Dataset S2), indicating concordance approaching 90%. It is also of relevance that the plastids analysed here were from light-grown cells only, and previous work has demonstrated that significant changes to protein composition are not accompanied by transcript changes: some proteins are therefore probably absent from the present plastid material (Ebenezer et al, 2019). This could arise partially as a result of N-terminal sequence truncation but could also signify our incomplete understanding of euglenid plastid-targeting signals.…”

“…To assess the completeness of the current dataset we found that 48/67 (72%) plastid encoded proteins were present. By contrast, only 474/1902 (25%) proteins in silico predicted as plastid-targeted from transcriptome data (Ebenezer et al, 2019) were detected by proteomics, and 871 proteins identified by proteomics were absent from this in silico set, suggesting that available prediction tools are inaccurate in the case of Euglena. By contrast, only 474/1902 (25%) proteins in silico predicted as plastid-targeted from transcriptome data (Ebenezer et al, 2019) were detected by proteomics, and 871 proteins identified by proteomics were absent from this in silico set, suggesting that available prediction tools are inaccurate in the case of Euglena.…”

“…Mass spectra were analysed using MAXQUANT (v.1.5, Cox & Mann, 2008), using the predicted translated transcriptome (GEFR00000000.1; Ebenezer et al, 2019). Each lane was divided into eight slices that were excised, destained and subjected to tryptic digestion and reductive alkylation.…”

“…Complex nutritional strategies and an ability to adapt to various environments are major features of the euglenids (Leander et al, 2001;Leander, 2004). Recent advances in defining the transcriptome and proteome of Euglena gracilis promises to improve understanding of the molecular mechanisms employed by this organism and its relatives (Ebenezer et al, 2019). Recent advances in defining the transcriptome and proteome of Euglena gracilis promises to improve understanding of the molecular mechanisms employed by this organism and its relatives (Ebenezer et al, 2019).…”