On the origin and evolution of RNA editing in metazoans.

Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed mRNAs is the hallmark of metazoan transcriptional regulation. Here, by profiling the RNA editomes of 22 species that cover major groups of Holozoa, we provide substantial evidence supporting A-to-I mRNA editing as a regulatory innovation originating in the last common ancestor of extant metazoans. This ancient biochemistry process is preserved in most extant metazoan phyla and primarily targets endogenous double-stranded RNA (dsRNA) formed by evolutionarily young repeats. We also find intermolecular pairing of sense-antisense transcripts as an important mechanism for forming dsRNA substrates for A-to-I editing in some but not all lineages. Likewise, recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing might first emerge as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.

Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum.

The marine ciliate Mesodinium rubrum is famous for its ability to acquire and exploit chloroplasts and other cell organelles from some cryptophyte algal species. We sequenced genomes and transcriptomes of free-swimming Teleaulax amphioxeia, as well as well-fed and starved M. rubrum in order to understand cellular processes upon sequestration under different prey and light conditions. From its prey, the ciliate acquires the ability to photosynthesize as well as the potential to metabolize several essential compounds including lysine, glycan, and vitamins that elucidate its specific prey dependency. M. rubrum does not express photosynthesis-related genes itself, but elicits considerable transcriptional control of the acquired cryptophyte organelles. This control is limited as light-dependent transcriptional changes found in free-swimming T. amphioxeia got lost after sequestration. We found strong transcriptional rewiring of the cryptophyte nucleus upon sequestration, where 35% of the T. amphioxeia genes were significantly differentially expressed within well-fed M. rubrum. Qualitatively, 68% of all genes expressed within well-fed M. rubrum originated from T. amphioxeia. Quantitatively, these genes contributed up to 48% to the global transcriptome in well-fed M. rubrum and down to 11% in starved M. rubrum. This tertiary endosymbiosis system functions for several weeks, when deprived of prey. After this point in time, the ciliate dies if not supplied with fresh prey cells. M. rubrum represents one evolutionary way of acquiring photosystems from its algal prey, and might represent a step on the evolutionary way towards a permanent tertiary endosymbiosis.

Studies on the genus Mesodinium II. Ultrastructural and molecular investigations of five marine species help clarifying the taxonomy.

We provide a detailed study of four marine Mesodinium species and compare the data to the companion article on Mesodinium chamaeleon and other available studies on Mesodinium, to shed some light on the taxonomy of the genus. Micrographs of two red phototrophic Mesodinium species, Mesodinium rubrum and Mesodinium major n. sp., as well as the first published micrographs of two heterotrophic species, M. pulex and M. pupula are presented in combination with molecular analyses based on the ribosomal genes. The main conclusion of this study is the invalidity of the genus Myrionecta based on the arrangements of the basal bodies forming the cirri and the separation of species formerly known as M. rubrum resulting in an emended description of M. rubrum and the description of a related new species M. major n. sp.

Studies on the genus Mesodinium I: ultrastructure and description of Mesodinium chamaeleon n. sp., a benthic marine species with green or red chloroplasts.

We provide here the description of a new marine species that harbors green or red chloroplasts. In contrast to certain other species of the genus, Mesodinium chamaeleon n. sp. can be maintained in culture for short periods only. It captures and ingests flagellates including cryptomonads. The prey is ingested very rapidly into a food vacuole without the cryptomonad flagella being shed and the trichocysts being discharged. The individual food vacuoles subsequently serve as photosynthetic units, each containing the cryptomonad chloroplast, a nucleus, and some mitochondria. The ingested cells are eventually digested. This type of symbiosis differs from other plastid-bearing Mesodinium spp. in retaining ingested cryptomonad cells almost intact. The food strategy of the new species appears to be intermediate between heterotrophic species, such as Mesodinium pulex and Mesodinium pupula, and species with red cryptomonad endosymbionts, such as Mesodinium rubrum.

Molecular evidence for host-symbiont specificity in soritid foraminifera.

Symbiosis between the dinoflagellate genus Symbiodinium and various invertebrates and protists is an ubiquitous phenomenon in shallow tropical and subtropical waters. Molecular studies undertaken on cnidarian symbionts revealed the presence of several distinctive lineages or subgeneric clades of Symbiodinium whose taxonomic level provides limited information about the specificity between invertebrate hosts and their symbionts. This contrasts with the finding of several Symbiodinium clades being present almost exclusively in foraminifera and belonging to the subfamily Soritinae. To test whether such specificity also exists at a lower taxonomic level within Soritinae, we obtained the SSU rDNA sequences from 159 soritid individuals collected in nine localities worldwide and representing all known morphospecies of this subfamily. For each individual, the symbionts were determined either by sequencing or by RFLP analysis. We distinguished 22 phylotypes of Soritinae in relation with a number of symbiont "groups" corresponding to 3 clades and 5 subclades of Symbiodinium. Among the 22 soritid phylotypes, 14 show strict symbiont specificity and only one was found to be a host for more than two "groups" of Symbiodinium. It is suggested that the strong host-symbiont specificity observed in Soritinae is a combined effect of a selective recognition mechanism, vertical transmission of symbionts, and biogeographical isolation.