Description: Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote–eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have 〈21, 000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph. © 2012 Macmillan Publishers Limited. All rights reserved.

Description: Chlorarachniophytes are unicellular marine algae with plastids (chloroplasts) of secondary endosymbiotic origin. Chlorarachniophyte cells retain the remnant nucleus (nucleomorph) and cytoplasm (periplastidial compartment, PPC) of the green algal endosymbiont from which their plastid was derived. To characterize the diversity of nucleus-encoded proteins targeted to the chlorarachniophyte plastid, nucleomorph, and PPC, we isolated plastid–nucleomorph complexes from the model chlorarachniophyte Bigelowiella natans and subjected them to high-pressure liquid chromatography-tandem mass spectrometry. Our proteomic analysis, the first of its kind for a nucleomorph-bearing alga, resulted in the identification of 324 proteins with 95% confidence. Approximately 50% of these proteins have predicted bipartite leader sequences at their amino termini. Nucleus-encoded proteins make up 〉90% of the proteins identified. With respect to biological function, plastid-localized light-harvesting proteins were well represented, as were proteins involved in chlorophyll biosynthesis. Phylogenetic analyses revealed that many, but by no means all, of the proteins identified in our proteomic screen are of apparent green algal ancestry, consistent with the inferred evolutionary origin of the plastid and nucleomorph in chlorarachniophytes.

Description: Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic analyses focused on Aquifex aeolicus identified Thermotogae and Aquificae either as successive early branches or sisters in a rooted bacterial phylogeny, but many phylogenies and cellular traits have suggested a stronger affiliation with the Epsilonproteobacteria. Different scenarios for the evolution of the Aquificae yield different phylogenetic predictions. Here, we outline these scenarios and consider the fit of the available data, including three sequenced Aquificae genomes, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the Epsilonproteobacteria have the strongest affinities with the three Aquificae analyzed. However, this pattern is shown by only a minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: Most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, whereas a wide range of metabolic and cellular processes strongly supported the link between Aquificae and Epsilonproteobacteria. Depending on which sets of genes are privileged, either Thermotogae or Epsilonproteobacteria is the most plausible adjacent lineage to the Aquificae. Both scenarios require massive sharing of genes to explain the history of this enigmatic group, whose history is further complicated by specific affinities of different members of Aquificae to different partner lineages.