Circular chloroplast chromosomes: the grand illusion.

If we could extract, purify, and visualize the intact DNA molecules from chloroplasts, what would those molecules look like? Most would expect to find circular DNA molecules the size of the chloroplast genome. By contrast, however, only a small fraction of the DNA obtained from chloroplasts is found as genome-sized circles. The reasons for this profound discrepancy are the subject of this article. I will trace the history of research on chloroplast DNA (cpDNA) to elucidate why it has taken more than 30 years to realize that the circle is not the principal form of DNA in chloroplasts and to examine the relationship between the chloroplast genome and the segregating genetic unit or chromosome in chloroplasts. The critical finding is that the chloroplast chromosome can contain many genome equivalents. I will also discuss the coupling between chromosomal replication and segregation in chloroplasts. To avoid confusion, I define some terms. The genome is the entire complement of genetic material in a virus, prokaryote, mitochondrion, or chloroplast or the haploid nuclear genetic complement of a eukaryotic species. A genome equivalent is the amount of DNA in a single copy of a genome. A chromosome is the segregating genetic unit that carries either a subset or all of the genome into each daughter cell or organelle during division. For example, the ant Myrmecia pilosula has a single pair of homologous chromosomes in the nucleus (Crosland and Crozier, 1986). The amount of DNA in a single chromosome equals the amount of DNA in the genome. In most ants and most eukaryotes, however, the DNA content of a single nuclear chromosome is less than that of the genome, and the DNA content of a segregating genetic unit never exceeds that of the genome. The genome in most bacteria, such as Escherichia coli, is contained on a single DNA-containing body known as the nucleoid. As a nucleoid segregates to daughter cells upon division, that nucleoid represents a bacterial chromosome. In contrast with what is found in the eukaryotic nucleus, however, the amount of DNA per bacterial chromosome in rapidly dividing cells is typically several to many times larger than one genome equivalent. As I will show, the situation in chloroplasts is similar to that in bacteria, and the size of the chloroplast chromosome is rarely as small as one genome equivalent.