The origin and early evolution of eukaryotic plastids

Project Information

PLAST-EVOL

Grant agreement ID: 787904

DOI

10.3030/787904

Project closed

EC signature date 7 June 2018

Start date 1 October 2018

End date 30 September 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 499 986,00

EU contribution

€ 2 499 986,00

Coordinated by

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France

Periodic Reporting for period 4 - PLAST-EVOL (The origin and early evolution of eukaryotic plastids)

Reporting period: 2023-04-01 to 2024-09-30

Summary of the context and overall objectives of the project

More than 1 Ga ago, an ancient eukaryote became photosynthetic by engulfing a cyanobacterium that evolved into the first plastid. This changed our planet: photosynthetic eukaryotes became major primary producers and biogeochemical players. From this endosymbiosis evolved green algae and plants, red algae, and glaucophytes. Later, secondary endosymbioses of red and green algae spread plastids in many other phyla. However, many aspects of this evolutionary history remain obscure. The identity of that cyanobacterium was a mystery until we recently found that it belonged to the Gloeomargaritales. Yet, why this original endosymbiosis was so successful is unknown. We hypothesize that the unusual capacity of Gloeomargaritales to produce intracellular carbonates allowed buffering the pH increase produced by photosynthetic C fixation, which was crucial before the host evolved active pH regulation.

To test this hypothesis and gain insight into the evolution of plastids, we propose to: 1) characterize the physiology of Gloeomargarita lithophora, the only isolated Gloeomargaritales; 2) obtain new genomic data from other Gloeomargaritales; 3) study the impact of cyanobacterial genes transferred to the host nuclear genomes; and 4) retrace the evolutionary history of these genes in secondary endosymbioses.

Our work has led to several conclusions. 1) We isolated new Gloeomargaritales and obtained new genome sequences. Their analysis supports that the ancestor of Gloeomargaritales was a freshwater thermophilic species with intracellular carbonates. The first photosynthetic eukaryotes probably also evolved in moderately hot freshwater environments. 2) We identified a large number of genes transferred from the plastids into the nuclear genomes of the eukaryotic hosts. They reveal a complex evolutionary history, in particular for secondary endosymbiosis. They were preceded by cryptic endosymbioses of red algae in the case of lineages with green secondary plastids, and occurred several times independently in lineages with red secondary plastids.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

- WP1: Intracellular carbonates and pH regulation as key permissive traits for the origin of plastids.
We isolated new Gloeomargaritales, including a new thermophilic one, and identified their growth conditions.
We characterized a new protein, calcyanin, involved in cellular calcium homeostasis and intracellular carbonate precipitation in Gloeomargaritales.

- WP2: Increasing the sampling of plastid-related cyanobacteria and their genomes.
We isolated the first thermophilic species, Gloeomargarita ahousahtiae, and characterized its phenotype and genome sequence. We also sequenced the genome of co-isolated parasitic bacteria.

We also assembled 11 new Gloeomargaritales genome sequences from various metagenomes. Their analysis indicates that the ancestral Gloeomargaritales were freshwater thermophilic species that synthesized intracellular carbonates. This, combined with phylogenetic analysis of photosynthetic eukaryotes, suggests that these eukaryotes also originated in moderately hot freshwater environments, instead of marine environments as previously thought.

- WP3: Reconstructing endosymbiotic gene transfer patterns in primary and secondary plastid endosymbiosis.

We sequenced the genomes of seven unicellular red algae to study the origin of red secondary plastids and the associated endosymbiotic gene transfers (EGTs). We also isolated five new non-photosynthetic species closely related to two major clades of secondary algae (chlorarachniophytes, with green plastids, and ochrophytes, with red plastids).
We analyzed the EGT events linked to the primary and secondary endosymbioses using our enriched collection of genome sequences. We detected ~900 EGT candidates, significantly increasing the number of previously detected EGT and allowing to better characterize the impact of plastid endosymbiosis on the host genomes. We discovered cryptic red algal endosymbioses in algae carrying green secondary plastids (chlorarachniophytes and euglenids), which appear to have facilitated the later acquisition of green plastids.
We characterized new protist species that feed on unicellular algae and that are closely related to the large photosynthetic clade of the Ochrophyta (containing well-known algae such as diatoms and kelp). These new species are excellent host models to understand the first steps in secondary plastid endosymbioses.

- WP4: Dating primary and secondary plastid endosymbioses with improved calibration points.

We have worked on species from groups with reliable fossil records to include new calibration points in molecular dating analyses. We sequenced the genomes of two coralline red algae and one dasycladales green alga and included them in a large plastid genome dataset of primary and secondary photosynthetic eukaryotes. Our molecular dating results validate previous inferences based on nuclear genome data but show better precision narrower for the inferred dates and higher stability in the presence or absence of specific fossil calibrations. The ancestors of the groups containing secondary red algal plastids appear to have coexisted during the early Neoproteorozoic (more than 1 Ga), making possible the complex series of endosymbiotic events that gave rise to these lineages.

Our main results have been published in peer-reviewed journals and are available on open-access platforms (Europe PMC https://europepmc.org/ and HAL https://cnrs.hal.science/). We also communicated them to the scientific community through international scientific meetings, and to the general public via public lectures and articles in the popular press -particularly those covering the expeditions in search of new cyanobacterial and algal species.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

We have been successful in the riskiest tasks of the project, notably the isolation of new Gloeomargaritales. We have also identified a new protein (calcyanin) that plays a key role in the biomineralization of intracellular carbonates in these species and regulates important metabolic traits that were probably involved in the endosymbiosis at the origin of plastids.

The expected results for the four WP of the project are:

- WP1:
Characterize new Gloeomargaritales species.
Elucidate the molecular mechanisms of the new protein calcyanin in carbonate biomineralization.

- WP2:
Carry out comparative genomic analyses of new Gloeomargaritales genome sequences. Identify the genes unique to them that may have been involved in plastid endosymbiosis.

- WP3:
Identify endosymbiotic gene transfers linked to primary and secondary plastid endosymbioses.

- WP4:
Characterize new reference plastid genomes of Corallinales and Dasycladales algae.
Infer the dates of primary and secondary plastid endosymbioses using molecular dating with new calibration points.

Samplig a microbial mat containing new Gloeomargaritales cyanobacteria