Dating the cyanobacterial ancestor of the chloroplast

Abstract

Cyanobacteria have had a pivotal role in the history of life on Earth being the first organisms to perform oxygenic photosynthesis, which changed the atmospheric chemistry and allowed the evolution of aerobic Eukarya. Chloroplasts are the cellular organelles of photoautotrophic eukaryotes in which most portions of photosynthesis occur. Although the initial suggestion that cyanobacteria are the ancestors of chloroplasts was greeted with skepticism, the idea is now widely accepted. Here we attempt to resolve and date the cyanobacterial ancestry of the chloroplast using phylogenetic analysis and molecular clocks. We found that chloroplasts form a monophyletic lineage, are most closely related to subsection-I, N2-fixing unicellular cyanobacteria (Order Chroococcales), and heterocyst-forming Order Nostocales cyanobacteria are their sister group. Nostocales and Chroococcales appeared during the Paleoproterozoic and chloroplasts appeared in the mid-Proterozoic. The capability of N2 fixation in cyanobacteria may have appeared only once during the late Archaean and early Proterozoic eons. Furthermore, we found that oxygen-evolving cyanobacteria could have appeared in the Archaean. Our results suggest that a free-living cyanobacterium with the capacity to store starch through oxygenic CO2 fixation, and to fix atmospheric N2, would be a very important intracellular acquisition, which, as can be recounted today from several lines of evidence, would have become the chloroplast by endosymbiosis.

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

“…The topology differs from two recent studies with different (23) or larger (24) species sampling than ours: in ref. 23 …”

“…Comparing the reconstructed relative chronology with two recent molecular dating studies by Falcon et al (23) and Blank et al (22), we find good agreement for early chronological relationships: both find that node 4, the ancestor of nodes 5 (clade containing Trichodesmium and Nostocales) and 6 (clade containing Synchocystis and Microcystis) is the first major group to emerge; both also support the order of nodes 5, 6, and 8, as well as the late diversification of the Synechococcus-Prochlorococcus group (nodes 13-15 and 17); this correspondence with our results is remarkable given that both studies rely on a relaxed molecular clock and calibration constraints based on the geological and The maximum likelihood time orders are indicated as node labels. Squares correspond to major diversification events discussed in the text.…”

“…In general a transfer belongs to multiple fields; for example, some of the transfers from within 4 to above 16 may be from within 5 to above 16. fossil records (three calibration points in ref. 23 and five in ref. 22), whereas our model uses neither.…”

Characterization and Evolution of Tetrameric Photosystem I from the Thermophilic Cyanobacterium Chroococcidiopsis sp TS-821

“…Deusch et al (2008) point out that heterocyst-forming cyanobacteria are the origin of plant plastids by comparing cyanobacterial and plant genomes. However, the placement of heterocyst-forming cyanobacteria as a likely progenitor to the plastid was questioned by Falcón et al (2010), pointing out the insufficient coverage of the cyanobacterial genome. Instead, Falcón et al conclude that unicellular nitrogen-fixing cyanobacteria (subsection I) are the closest relative to plastids according to the phylogenetic trees built based on 16S RNA and rbcL sequences (Falcón et al, 2010), while other studies support the idea that plastids originated from nitrogen-fixing cyanobacteria (Gupta, 2009;Criscuolo and Gribaldo, 2011;Hackenberg et al, 2011;Kern et al, 2011).…”

Diversification of DnaA dependency for DNA replication in cyanobacterial evolution

“…To determine whether dnaA is universally required for DNA replication, we constructed dnaA deletion Diversification of cyanobacterial DNA replication R Ohbayashi et al mutants in model cyanobacteria Synechocystis and Anabaena that are more closely related to chloroplasts than S. elongatus, as shown in a phylogenetic tree (Turner et al, 1999;Falcon et al, 2010;Shih et al, 2013;Ochoa de Alda et al, 2014) (Figure 5a and Supplementary Figure S6). We readily obtained dnaA deletion mutants using Synechocystis and Anabaena, in contrast to S. elongatus.…”