Translation and Translational Control in Dinoflagellates

Abstract

Dinoflagellates are unicellular protists that feature a multitude of unusual nuclear features, including large genomes, packaging of DNA without histones, and multiple gene copies organized as tandem gene arrays. Furthermore, all dinoflagellate mRNAs experience trans-splicing with a common 22-nucleotide splice leader (SL) sequence. These features challenge some of the concepts and assumptions about the regulation of gene expression derived from work on model eukaryotes such as yeasts and mammals. Translational control in the dinoflagellates, based on extensive study of circadian bioluminescence and by more recent microarray and transcriptome analyses, is now understood to be a crucial element in regulating gene expression. A picture of the translation machinery of dinoflagellates is emerging from the recent availability of transcriptomes of multiple dinoflagellate species and the first complete genome sequences. The components comprising the translational control toolkit of dinoflagellates are beginning to take shape and are outlined here.

Keywords: dinoflagellate; gene expression; post-transcriptional control; translation factors.

Figure 1

A schematic view of the factors involved in eukaryotic translation initiation. Transcripts (in blue) are present in the cytoplasm as a complex with the poly(A) binding protein (PABP), the cap-binding protein eIF4E, the scaffold protein eIF4G (linking PABP with the cap-binding protein) and two other initiation factors eIF4A and eIF4B. The 43S pre-initiation complex (43S PIC) is formed when the small ribosome subunit (yellow) in a complex with initiation factors eIF1, 1A, 3 and 5 binds the trimeric eIF2, which contains a tRNA charged with methionine (Met-tRNA_i). The small ribosome subunit moves down the RNA sequence until the anticodon on the Met-tRNA_i recognizes and binds the AUG start codon. This recognition allows hydrolysis of the GTP bound to eIF2, causing release of the eIF2 from the PIC along with the eIF1, eIF1A, eIF3 and eIF5. The GTP-bound form of eIF2 is regenerated by the guanine exchange factor eIF2B. Translation can be globally downregulated by phosphorylation of eIF2α, which then tightly binds eIF2B thus impeding recycling of eIF2. Orthologues for a GCN-type eIF2α kinase and the cap-binding regulatory protein 4E-BP have not been identified in the dinoflagellate transcriptome sequence assembly (TSA).

Figure 2

A list of eukaryotic initiation factors from Arabidopsis thaliana was used to query the dinoflagellate TSA using tBLASTn. Query sequences are listed at right, and the range of e-values (from e⁻¹²⁰ to 1) are shown as horizontal red bars; an asterisk at left indicates an e-value of 0. The number of species in which hits were recovered is indicated by the color in the bar. Most of the eIF2B subunits are not found in dinoflagellates. Factors eIF4E. eIF4G and eIF5 are incomplete, suggesting their normal function may be complemented by different proteins in dinoflagellates.

Figure 3

A 130-amino acid conserved core of the mammalian eIF4E1A (subclade1a) illustrating the important binding regions for the m⁷G cap and eIF4G. The eight conserved tryptophan residues (numbered as for the mammalian sequence) are shown in black along with the residues that are found at the corresponding positions in representative sequences from the three dinoflagellate clades. Residues in yellow are important for binding the phosphates of the m⁷G (the aspartate at position 90 coordinates binding by arginine-157), while the eIF4G binding motif (S/TVxxFW) is shown in blue. The small v in the eIF4G binding motif could also be T (for clade 2) or A (for clade 3). The glutamate at position 103 (red) is involved in hydrogen bonding to the m7G. Note that dinoflagellate clade 1 eIF4Es have an insertion of 12–13 amino acids between W73 and W102, as well as an insertion of 7–9 amino acids between W130 and W166. Figure based on [126].

Figure 4

A list of RNA-binding proteins from mammalian cells was used to query the dinoflagellate TSA using tBLASTn, Individual species were queried one-by-one, and the best e-value recorded for each species. Mouse proteins (except where indicated) selected as representatives for the different domains are RRM, polyadenylate-binding protein 1; KH, Plasmodium PF3D7_0605100; ZnF-CCCH, splicing factor U2AF 35 kDa subunit; ZnF-CCHC, protein lin-28 homolog; dsRNA, E. coli Rnase III; OB NTP-binding, ATP-dependent RNA helicase A; SAP, heterogeneous nuclear ribonucleoprotein U; LSM, LSM14 homolog; YTH, YTH domain-containing family protein; S1, ATP-dependent RNA helicase DHX8; PWI, serine/arginine repetitive matrix protein; eIF4G, eukaryotic translation initiation factor 4 gamma; La, lupus La.