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The amazing journey of the chloroplast genome: how to change from circular to linear?
Chloroplast genome (cpDNA), also known as plastid DNA (ptDNA), is DNA located in chloroplasts, the photosynthetic organelles within the cells of some eukaryotes. Unlike the genome in the nucleus, chloroplasts have a separate genome. In 1959, scientists confirmed the existence of chloroplast DNA from a biochemical perspective for the first time, and in 1962, this discovery was confirmed again through electron microscope observation.
“Chloroplasts are considered semi-autonomous and have the ability to synthesize proteins on their own.”
With the advancement of technology, in 1986, scientists completed the first complete chloroplast genome sequence analysis for tobacco (Nicotiana tabacum) and liverwort (Marchantia polymorpha). Since then, the scientific community has sequenced tens of thousands of chloroplast genomes from different species, revealing the continuous evolution of chloroplast genome structure and function.
From circle to line - structural changes in chloroplast DNA
Traditional wisdom holds that most chloroplast DNA has a circular structure, usually between 120,000 and 170,000 base pairs. However, recent studies have shown that the chloroplast DNA of certain plants may exist more in a linear form. In fact, in corn chloroplasts, 95% of the DNA appears in a branched linear form, which overturns the previous view of being circular.
"In fact, more than 95% of maize chloroplast DNA is observed in branched linear forms rather than individual circles."
Inverted repeats and gene function
Many chloroplast DNAs possess two inverted repeats that separate long single copy regions (LSC) from short single copy regions (SSC). The length of inverted repeats tends to vary widely between species, generally ranging from 4,000 to 25,000 base pairs. In plants, these repeats typically accumulate genes conservatively and undergo relatively few mutations.
Not only are these inverted repeat regions important in plants, but they also reflect the presence of similar structures in cyanobacteria and two other chloroplast lineages, such as cyanobacteria and red algae, suggesting that these repeat structures existed early in evolution. .
Gene content and gene expression
By sequencing more than 5,000 chloroplast genomes, we can further understand their genetic content. The chloroplast genome of most plants encodes approximately 120 genes, which are mainly involved in the core components of photosynthesis and factors affecting their expression and assembly.
“For most plant species, the core genes encoded by their chloroplast genomes are quite conserved.”
Chloroplast genome reduction and gene transfer
Over time, parts of many chloroplast genomes are transferred to the host cell nucleus, a process known as endosymbiotic gene transfer. As a result of this process, the chloroplast genome is significantly reduced compared to free-living cyanobacteria, typically containing only 60 to 100 genes.
Nonetheless, in some cases genes are transferred from bacteria into chloroplasts. This reflects the importance of chloroplasts in the evolution of host cells, to the extent that in some cases chloroplast genes survive in the host's nucleus even though the chloroplasts themselves no longer exist.
Chloroplast protein synthesis and regulation
95% of approximately three thousand chloroplast proteins are encoded by nuclear genes, which requires coordinated synthesis of chloroplast proteins. Protein synthesis within chloroplasts relies primarily on RNA polymerases encoded by nuclear genes that are structurally similar to those found in bacteria. Chloroplasts also contain a mysterious second RNA polymerase, encoded by the plant's nuclear genes.
In the process of protein synthesis, RNA editing machinery also plays an important role in chloroplasts, which allows post-transcriptional repair to effectively protect functional sequences. Research shows that in highly oxidative environments, the efficiency of RNA editing increases, reflecting further demands on gene stability.
Chloroplast DNA replication mechanism
As for the replication mechanism of chloroplast DNA, it has not yet been fully established, but two models have been proposed in the mainstream. One model is double-displacement loop (D-loop) replication, while the second emphasizes that most cpDNA adopts a linear structure and undergoes homologous recombination during replication. Competition between the two models continues, but new research points out that many cpDNAs may undergo structural changes that affect mechanisms related to gene replication.
Many mysteries about the chloroplast genome remain to be solved. In future studies, can we draw a clearer picture of the evolution of chloroplast DNA?
