Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote

Abstract

Chloroplasts in photosynthetic eukaryotes originated from a cyanobacterial endosymbiosis far more than 1 billion years ago1-3. Due to this ancientness, it remains unclear how this evolutionary process proceeded. To unveil this mystery, we analysed the whole genome sequence of a photosynthetic rhizarian amoeba4, Paulinella micropora5,6, which has a chloroplast-like organelle that originated from another cyanobacterial endosymbiosis7-10 about 0.1 billion years ago11. Here we show that the predacious amoeba that engulfed cyanobacteria evolved into a photosynthetic organism very quickly in the evolutionary time scale, probably aided by the drastic genome reorganization activated by large DNA virus. In the endosymbiotic evolution of eukaryotic cells, gene transfer from the endosymbiont genome to the host nucleus is essential for the evolving host cell to control the endosymbiont-derived organelle12. In P. micropora, we found that the gene transfer from the free-living and endosymbiotic bacteria to the amoeba nucleus was rapidly activated but both simultaneously ceased within the initiation period of the endosymbiotic evolution, suggesting that the genome reorganization drastically proceeded and completed. During this period, large DNA virus appeared to have infected the amoeba, followed by the rapid amplification and diversification of virus-related genes. These findings led us to re-examine the conventional endosymbiotic evolutionary scenario that exclusively deals with the host and the symbiont, and to extend it by incorporating a third critical player, large DNA virus, which activates the drastic gene transfer and genome reorganization between them. This Paulinella version of the evolutionary hypothesis deserves further testing of its generality in evolutionary systems and could shed light on the unknown roles of large DNA viruses13 in the evolution of terrestrial life.

Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis

“…2016 ) to MYN1 Scaffold1104 that is enriched in Maverick/Polinton-type transposons (see fig. 3 A in Matsuo et al. 2019 ).…”

“…A recent analysis of the genome of the closely related strain P. micropora MYN1 (hereafter, MYN1) led to the hypothesis that large double-stranded DNA (dsDNA) viruses may have facilitated early gene transfer events to the amoeba nucleus, allowing rapid integration of the chromatophore ( Matsuo et al. 2019 ).…”

“…2003 ). In contrast to this model of chromatophore genome reduction driven by neutral processes, Matsuo et al proposed that large DNA viruses containing Maverick/Polinton-type transposons may have infected the amoeba lineage at the time of endosymbiosis and acted as vectors of both EGT and HGT to the nucleus ( Matsuo et al. 2019 ).…”

Why is primary endosymbiosis so rare?

“…micropora KR01 (hereafter, KR01; Lhee et al ., 2021a) to 967 Mbp in P . micropora MYN1 (Matsuo et al ., 2019), and c . 10 Gbp in the more distantly related P .…”

“…The EGT‐derived hli in photosynthetic Paulinella has undergone extensive expansion with 51 copies in KR01 and 64 in P . micropora MYN1 (Matsuo et al ., 2019; Lhee et al ., 2021a), compared with 13 copies in free‐living Synechococcus sp. WH 5701.…”