Chloroplast DNA Replication Is Regulated by the Redox State Independently of Chloroplast Division in Chlamydomonas reinhardtii

Chloroplasts arose from a cyanobacterial endosymbiont and multiply by division. In algal cells, chloroplast division is regulated by the cell cycle so as to occur only once, in the S phase. Chloroplasts possess multiple copies of their own genome that must be replicated during chloroplast proliferation. In order to examine how chloroplast DNA replication is regulated in the green alga Chlamydomonas reinhardtii, we first asked whether it is regulated by the cell cycle, as is the case for chloroplast division. Chloroplast DNA is replicated in the light and not the dark phase, independent of the cell cycle or the timing of chloroplast division in photoautotrophic culture. Inhibition of photosynthetic electron transfer blocked chloroplast DNA replication. However, chloroplast DNA was replicated when the cells were grown heterotrophically in the dark, raising the possibility that chloroplast DNA replication is coupled with the reducing power supplied by photosynthesis or the uptake of acetate. When dimethylthiourea, a reactive oxygen species scavenger, was added to the photoautotrophic culture, chloroplast DNA was replicated even in the dark. In contrast, when methylviologen, a reactive oxygen species inducer, was added, chloroplast DNA was not replicated in the light. Moreover, the chloroplast DNA replication activity in both the isolated chloroplasts and nucleoids was increased by dithiothreitol, while it was repressed by diamide, a specific thiol-oxidizing reagent. These results suggest that chloroplast DNA replication is regulated by the redox state that is sensed by the nucleoids and that the disulfide bonds in nucleoid-associated proteins are involved in this regulatory activity.Chloroplasts are semiautonomous organelles that possess their own genome, which is complexed with proteins to form nucleoids and also certain machinery needed for protein synthesis, as is the case in prokaryotes. It is generally accepted that chloroplasts arose from a bacterial endosymbiont closely related to the currently extant cyanobacteria (Archibald, 2009; Keeling, 2010). In a manner reminiscent of their free-living ancestor, chloroplasts proliferate by the division of preexisting organelles that are coupled to the duplication and segregation of the nucleoids (Kuroiwa, 1991) and have retained the bulk of their bacterial biochemistry. However, chloroplasts have subsequently been substantially remodeled by the host cell so as to function as complementary organelles within the eukaryotic host cell (Rodríguez-Ezpeleta and Philippe, 2006; Archibald, 2009; Keeling, 2010). For example, most of the genes that were once in the original endosymbiont genome have been either lost or transferred into the host nuclear genome. As a result, the size of the chloroplast genome has been reduced to less than one-tenth that of the free-living cyanobacterial genome. Thus, the bulk of the chloroplast proteome consists of nucleus-encoded proteins that are translated on cytoplasmic ribosomes and translocated into chloroplasts. In addition, chloroplast division ultimately came to be a process tightly regulated by the host cell, which ensured permanent inheritance of the chloroplasts during the course of cell division and from generation to generation (Rodríguez-Ezpeleta and Philippe, 2006; Archibald, 2009; Keeling, 2010).Chloroplast division is performed by constriction of the ring structures at the division site, encompassing both the inside and the outside of the two envelopes (Yang et al., 2008; Maple and Møller, 2010; Miyagishima, 2011; Pyke, 2013). One part of the division machinery is derived from the cyanobacterial cytokinetic machinery that is based on the FtsZ protein. In contrast, other parts of the division machinery involve proteins specific to eukaryotes, including one member of the dynamin family. The majority of algae (both unicellular and multicellular), which diverged early within the Plantae, have just one or at most only a few chloroplasts per cell. In algae, the chloroplast divides once per cell cycle before the host cell completes cytokinesis (Suzuki et al., 1994; Miyagishima et al., 2012). In contrast, land plants and certain algal species contain dozens of chloroplasts per cell that divide nonsynchronously, even within the same cell (Boffey and Lloyd, 1988). Because land plants evolved from algae, there is likely to have been a linkage between the cell cycle and chloroplast division in their algal ancestor that was subsequently lost during land plant evolution. Our recent study showed that the timing of chloroplast division in algae is restricted to the S phase by S phase-specific formation of the chloroplast division machinery, which is based on the cell cycle-regulated expression of the components of the chloroplast division machinery (Miyagishima et al., 2012).Because chloroplasts possess their own genome, chloroplast DNA must be duplicated so that each daughter chloroplast inherits the required DNA after division. However, it is still unclear how the replication of chloroplast DNA is regulated and whether the replication is coupled with the timing of chloroplast division, even though certain studies have addressed this issue, as described below.Bacteria such as Escherichia coli and Bacillus subtilis possess a single circular chromosome. In these bacteria, the process of DNA replication is tightly coupled with cell division (Boye et al., 2000; Zakrzewska-Czerwińska et al., 2007), in which the initiation of replication is regulated such that it occurs only once per cell division cycle (Boye et al., 2000). In contrast, cyanobacteria contain multiple copies of their DNA (e.g. three to five copies in Synechococcus elongatus PCC 7942; Mann and Carr, 1974; Griese et al., 2011). In some obligate photoautotrophic cyanobacterial species, replication is initiated only when light is available (Binder and Chisholm, 1990; Mori et al., 1996; Watanabe et al., 2012). Replication is initiated asynchronously among the multiple copies of the DNA. Although the regulation of the initiation of DNA replication is less stringent than that in E. coli and B. subtilis, as described above, a recent study using S. elongatus PCC 7942 showed that this replication peaks prior to cell division, as in other bacteria.Chloroplasts also contain multiple copies of DNA (approximately 1,000 copies; Boffey and Leech, 1982; Miyamura et al., 1986; Baumgartner et al., 1989; Oldenburg and Bendich, 2004; Oldenburg et al., 2006; Shaver et al., 2008). In algae, chloroplast DNA is replicated in a manner that keeps pace with chloroplast and cell division in order to maintain the proper DNA content per chloroplast (i.e. per cell). In contrast, in land plants, the copy number of DNA in each chloroplast (plastid) changes during the course of development and differentiation, although contradictory results were reported about leaf development (Lamppa and Bendich, 1979; Boffey and Leech, 1982; Hashimoto and Possingham, 1989; Kuroiwa, 1991; Rowan and Bendich, 2009; Matsushima et al., 2011). Previous studies that synchronized the algal cell cycle by means of a 24-h light/dark cycle showed that chloroplast DNA is replicated only during the G1 phase, after which it is separated into daughter chloroplasts during the S phase by chloroplast division, implying that chloroplast DNA replication and division are temporally separated (Chiang and Sueoka, 1967; Grant et al., 1978; Suzuki et al., 1994). However, under these experimental conditions, G1 cells grow and the chloroplast DNA level increases during the light period. Cells enter into the S phase, chloroplast DNA replication ceases, and the chloroplasts divide at the beginning of the dark period. Thus, it is still unclear whether chloroplast DNA replication is directly controlled by the cell cycle, as is the case in chloroplast division, or chloroplast DNA replication occurs merely when light energy is available.We addressed this issue using a synchronous culture as well as a heterotrophic culture of the mixotrophic green alga Chlamydomonas reinhardtii. The results show that chloroplast DNA replication occurs independently of either the cell cycle or the timing of chloroplast division. Instead, it is shown that chloroplast DNA replication occurs when light is available in photoautotrophic culture and even under darkness in heterotrophic culture. Further experimental results suggest that chloroplast DNA replication is regulated by the redox state in the cell, which is sensed by the chloroplast nucleoids.