Interestingly, the system used to target proteins to 3 membrane plastids is also different in subtle but important ways to that of canonical secondary plastids with 4 enveloping membranes, and the same variations have been adopted in dinoflagellates and euglenophytes. The N-terminal leaders that direct proteins to canonical secondary plastids include a signal peptide (to enter the endomembrane system) and a transit peptide (to cross the 2 plastid membranes), and are similar in secondarily derived red and green plastids. In dinoflagellates and euglenophytes, however, an additional hydrophobic domain is found following the transit peptide of some, but intriguingly not all, proteins (Patron et al., 2005; Durnford and Gray, 2006). This domain is thought to anchor the proteins in the endomembrane, so as the protein moves through the Golgi apparatus the leader lays in the lumen but the mature protein remains in the cytosol (Sulli et al., 1999; Nassoury et al., 2003). The number of membranes and these unusual characteristics of targeting have both evolved convergently in dinoflagellates and euglenophytes, which suggests some link in how these 2 features evolved. Unfortunately, the mechanism by which proteins cross the membrane that is missing in both dinoflagellates and euglenophytes (the plasma membrane of the engulfed alga) is the most poorly understood step in the targeting pathway to canonical secondary plastids, so any specific model for preconditioning would be highly speculative.

The mitochondrial genomes of dinoflagellates and kinetoplastids are both highly unorthodox, and once again have evolved some unique features and several common complex characteristics. The kinetoplastid mitochondrion contains uniquely structured, protein-rich mitochondrial ribosomes with a reduced RNA component, unusual fatty acid synthesis and respiratory complexes such as the prokaryotic-like complex I, alternative terminal oxidase, massive tRNA import, and incomplete Krebs cycle. The complex genome of the kinetoplastid mitochondrion is known as kinetoplast DNA or kDNA, its genes being subjected to unprecedented levels of RNA editing (Fig. 4.4) (Lukeš et al., 2005). Dinoflagellate mitochondria have received far less attention, but it is now emerging that their genomes have also evolved a number of highly unusual characteristics, including trans-splicing, tRNA import, fragmented rRNAs, the loss of start and stop codons, and an oligouridine tail (Slamovits et al., 2007; Nash et al., 2008). Most strikingly, however, the structure of dinoflagellate mitochondrial genomes has also broken down into many fragments, the transcripts of which have high levels of RNA editing; however, as we discuss below, the details of both systems differ between kinetoplastids and dinoflagellates (Fig. 4.4).