Chloroplast DNA

Chloroplast DNA
Chloroplast DNA
Plants are unique among higher organisms in that they meet their energy needs through photosynthesis. The specific location for photosynthesis in plant cells is the chloroplast, which also contains a single, circular chromosome composed of DNA. Chloroplast DNA contains many of the genes necessary for proper chloroplast functioning.

A better understanding of the genes in chloroplast deoxyribonucleic acid (cpDNA) has improved the understanding of photosynthesis, and analysis of the deoxyribonucleic acid (DNA) sequence of these genes has been useful in studying the evolutionary history of plants.

Discovery of Chloroplast Genes

The work of nineteenth century Austrian botanist Gregor Mendel showed that the inheritance of genetic traits follows a predictable pattern and that the traits of offspring are determined by the traits of the parents.

For example, if the pollen from a tall pea plant is used to pollinate the flowers of a short pea plant, all the offspring are tall. If one of these tall offspring is allowed to self-pollinate, it produces a mixture of tall and short offspring, three-quarters of them tall and one-quarter of them short.


Similar patterns are observed for large numbers of traits from pea plants to oak trees. Because of the widespread application of Mendel’s work, the study of genetic traits by controlled mating is often referred to as Mendelian genetics.

In 1909 German botanist Karl Erich Correns discovered a trait in the four-o’clock plants (Mirabilis jalapa) that appeared to be inconsistent with Mendelian inheritance patterns.

He discovered that four-o’clock plants had a mixture of leaf colors on the same plant: Some were all green, many were partly green and partly white (variegated), and some were all white.

If he took pollen from a flower on a branch with all-green leaves and used it to pollinate a flower on a branch with all-white leaves, all the resulting seeds developed into plants with white leaves.

Likewise, if he took pollen from a flower on a branch with all-white leaves and used it to pollinate a flower on a branch with all-green leaves, all the resulting seeds developed into plants with green leaves.

Repeated pollen transfers in any combination always resulted in offspring whose leaves resembled those on the branch containing the flower that received the pollen, that is, the maternal parent. These results could not be explained by Mendelian genetics.

Since Correns’s discovery, many other such traits have been discovered. It is now known that the reason these traits do not follow Mendelian inheritance patterns is that their genes are not on the chromosomes in the nucleus of the cell where most genes are located. Instead, the gene for the four o’clock leaf color trait is located on the single, circular chromosome found in chloroplasts.

Because chloroplasts are specialized for photosynthesis, many of the genes on the single chromosome produce proteins or ribonucleic acid (RNA) that either directly or indirectly affect synthesis of chlorophyll, the pigment primarily responsible for trapping energy from light.

Because chlorophyll is green and because mutations in many chloroplast genes cause chloroplasts to be unable to make chlorophyll, most mutations result in partially or completely white or yellow leaves.

Identity of Chloroplast Genes

Advances in molecular genetics have allowed scientists to take a much closer look at the chloroplast genome. The size of the genome has been determined for a number of plants and algae and ranges from 85 to 292 kilobase pairs (one kb equals one thousand base pairs), with most being between 120 kb and 160 kb. The complete DNA sequences for several different chloroplast genomes of plants and algae have been determined.

Although a simple sequence does not necessarily identify the role of each gene, it has allowed the identity of a number of genes to be determined, and it has allowed scientists to estimate the total number of genes. In terms of genome size, chloroplast genomes are relatively small and contain slightly more than one hundred genes.

Roughly half of the chloroplast genes produce either RNA molecules or polypeptides that are important for protein synthesis. Some of the RNA genes occur twice in the chloroplast genomes of almost all land plants and some groups of algae.

The products of these genes represent all the ingredients needed for chloroplasts to carry out transcription and translation of their own genes. Half of the remaining genes produce polypeptides directly required for the biochemical reactions of photosynthesis.

What is unusual about these genes is that their products represent only a portion of the polypeptides required for photosynthesis. For example, the very important enzyme ATPase, the enzyme that uses proton gradient energy to produce the important energy molecule adenosine triphosphate (ATP), comprises nine different polypeptides.

Six of these polypeptides are products of chloroplast genes, but the other three are products of nuclear genes that must be transported into the chloroplast to join with the other six polypeptides to make active ATPase.

Another notable example is the enzyme ribulose biphosphate carboxylase (RuBP carboxylase), which is composed of two polypeptides. The larger polypeptide, called rbcL, is a product of a chloroplast gene, whereas the smaller polypeptide is the product of a nuclear gene.

The last thirty or so genes remain unidentified. Their presence is inferred because they have DNA sequences that contain all the components found in active genes. These kinds of genes are often called “open reading frames” (ORFs) until the functions of their polypeptide products are identified.

Impact and Applications

The discovery that chloroplasts have their own DNA and the further elucidation of their genes have had some impact on horticulture and agriculture.

Several unusual, variegated leaf patterns and certain mysterious genetic diseases of plants are now better understood. The discovery of some of the genes that code for polypeptides required for photosynthesis has helped increase understanding of the biochemistry of photosynthesis.

The discovery that certain key chloroplast proteins, such as ATPase and RuBP carboxylase, are composed of a combination of polypeptides coded by chloroplast and nuclear genes also raises some as yet unanswered questions.

For example, why would an important plant structure like the chloroplast have only part of the genes it needs to function? Moreover, if chloroplasts, as evolutionary theory suggests, were once free-living bacteria-like cells, which must have had all the genes needed for photosynthesis, why and how did they transfer some of their genes into the nuclei of the cells in which they are now found?

Of greater importance has been the discovery that the DNA sequences of many chloroplast genes are highly conserved; that is, they have changed very little during their evolutionary history. This fact has led to the use of chloroplast gene DNA sequences for reconstructing the evolutionary history of various groups of plants.

Traditionally, plant systematists (scientists who study the classification and evolutionary history of plants) have used structural traits of plants, such as leaf shape and flower anatomy, to try to trace the evolutionary history of plants.

Unfortunately, there are a limited number of structural traits, and many of them are uninformative or even misleading when used in evolutionary studies. These limitations are overcome when gene DNA sequences are used.

A DNA sequence of a few hundred base pairs in length provides the equivalent of several hundred traits, many more than the limited number of structural traits available (typically much fewer than one hundred).

One of the most widely used sequences is the rbcL gene. It is one of the most conserved genes in the chloroplast genome, which in evolutionary terms means that even distantly related plants will have a similar base sequence.

Therefore, rbcL can be used to retrace the evolutionary history of groups of plants that are very divergent from one another. The rbcL gene, along with a few other very conservative chloroplast genes, has already been used in attempts to answer some basic plant evolution questions about the origins of some of the major flowering plant groups.

Less conservative genes and ORFs show too much evolutionary change to be used at higher classification levels but are extremely useful in answering questions about the origins of closely related species, genera, or even families. As analytical techniques are improved, chloroplast genes show promise of providing even better insights into plant evolution.

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