Retrotransposition facilitated the establishment of a primary plastid in the thecate amoeba Paulinella

Evidence of a putative CO2 delivery system to the chromatophore in the photosynthetic amoeba Paulinella

The photosynthetic amoeba, Paulinella provides a recent (ca. 120 Mya) example of primary plastid endosymbiosis. Given the extensive data demonstrating host lineage-driven endosymbiont integration, we analysed nuclear genome and transcriptome data to investigate mechanisms that may have evolved in Paulinella micropora KR01 (hereinafter, KR01) to maintain photosynthetic function in the novel organelle, the chromatophore. The chromatophore is of α-cyanobacterial provenance and has undergone massive gene loss due to Muller's ratchet, but still retains genes that encode the ancestral α-carboxysome and the shell carbonic anhydrase, two critical components of the biophysical CO2 concentrating mechanism (CCM) in cyanobacteria. We identified KR01 nuclear genes potentially involved in the CCM that arose via duplication and divergence and are upregulated in response to high light and downregulated under elevated CO2. We speculate that these genes may comprise a novel CO2 delivery system (i.e., a biochemical CCM) to promote the turnover of the RuBisCO carboxylation reaction and counteract photorespiration. We posit that KR01 has an inefficient photorespiratory system that cannot fully recycle the C2 product of RuBisCO oxygenation back to the Calvin-Benson cycle. Nonetheless, both these systems appear to be sufficient to allow Paulinella to persist in environments dominated by faster-growing phototrophs.

Back to primary endosymbiosis: from plastids to artificial photosynthetic life-forms

Throughout evolution, only two known primary photosynthetic endosymbiosis occurred, which originated the Archaeplastida and the Paulinella spp. Fundamental questions regarding primary endosymbiosis remain unsolved, but may now be addressed with the recent development of chimeric photosynthetic life-form. Cournoyer et al. could establish artificial photosynthetic endosymbiosis between yeast and cyanobacteria.

The power of "controllers": Transposon-mediated duplicated genes evolve towards neofunctionalization

Since the discovery of the first transposon by Dr. Barbara McClintock, the prevalence and diversity of transposable elements (TEs) have been gradually recognized. As fundamental genetic components, TEs drive organismal evolution not only by contributing functional sequences (e.g., regulatory elements or "controllers" as phrased by Dr. McClintock) but also by shuffling genomic sequences. In the latter respect, TE-mediated gene duplications have contributed to the origination of new genes and attracted extensive interest. In response to the development of this field, we herein attempt to provide an overview of TE-mediated duplication by focusing on common rules emerging across duplications generated by different TE types. Specifically, despite the huge divergence of transposition machinery across TEs, we identify three common features of various TE-mediated duplication mechanisms, including end bypass, template switching, and recurrent transposition. These three features lead to one common functional outcome, namely, TE-mediated duplicates tend to be subjected to exon shuffling and neofunctionalization. Therefore, the intrinsic properties of the mutational mechanism constrain the evolutionary trajectories of these duplicates. We finally discuss the future of this field including an in-depth characterization of both the duplication mechanisms and functions of TE-mediated duplicates.

Algae obscura: The potential of rare species as model systems

Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems.

Endosymbiotic ratchet accelerates divergence after organelle origin: The Paulinella model for plastid evolution: The Paulinella model for plastid evolution

We hypothesize that as one of the most consequential events in evolution, primary endosymbiosis accelerates lineage divergence, a process we refer to as the endosymbiotic ratchet. Our proposal is supported by recent work on the photosynthetic amoeba, Paulinella, that underwent primary plastid endosymbiosis about 124 Mya. This amoeba model allows us to explore the early impacts of photosynthetic organelle (plastid) origin on the host lineage. The current data point to a central role for effective population size (N_e ) in accelerating divergence post-endosymbiosis due to limits to dispersal and reproductive isolation that reduce N_e , leading to local adaptation. We posit that isolated populations exploit different strategies and behaviors and assort themselves in non-overlapping niches to minimize competition during the early, rapid evolutionary phase of organelle integration. The endosymbiotic ratchet provides a general framework for interpreting post-endosymbiosis lineage evolution that is driven by disruptive selection and demographic and population shifts. Also see the video abstract here: https://youtu.be/gYXrFM6Zz6Q.