|
|
|
|
Gene
Content
and
Arrangement -
Chloroplast DNA encodes a complete set of ribosomal RNAs and tRNAs as well as many proteins. The ribosomal RNA genes are contained in the inverted .repeat and thus are present in two copies per genome. They are organized into an operon which has many similarities to bacterial rRNA operons. About 40 tRNAs, including acceptors for all twenty amino acids, have been identified and mapped in the chloroplast genomes of several species of plants.
|
Although tRNA genes are arranged in clusters in the Euglena chloroplast genome, they are dispersed throughout the genome of higher plants. An exception is the presence of two tRNA genes in the transcribed spacer on the 5' end of the rRNA operon.
Complete DNA sequences for entire chloroplast genomes are now available and so it is possible to determine the number of genes more precisely.
Computers are used to search the data for sequences with the properties of genes, for example "open reading frames" which contain a series of amino acid codons beginning with an initiation codon and ending with a termination codon and sequences that are homologous to known tRNA genes. It is possible from such work to predict the presence of more than 120 genes. About thirty of these are tRNA genes and another four encode ribosomal RNAs. There are about 85 protein coding genes.
|
Most of these encode proteins that have been identified in chloroplasts or are similar to proteins identified in other organisms, such as ribosomal proteins and RNA polymerase subunits.
Some of the protein coding genes which have been mapped on the chloroplast genome in one or more species of higher plants are listed in plants are listed
All green plants for which we have information contain essentially the same set of genes in their chloroplast genomes. The reason for this similarity is not immediately obvious. One possible explanation is based on the widely accepted notion that chloroplasts arose from cyanobacterial endosymbionts.
|
|
Since cyanobacterial genomes are some 20-30 times larger than those of chloroplasts, a dramatic reduction in the plastid genome must have occurred after the endosymbiotic association was established. If this reduction occurred quite soon after the original endosymbiosis and prior to the divergence of lineages leading to different groups of green plants, the similarity of green plant chloroplast genomes might reflect common ancestry.
On the other hand, one might postulate that certain genes are retained in the chloroplast genome for reasons of function. For example, genes for ribosomal and transfer RNAs may have been retained in the chloroplast cause it is difficult or impossible to transport RNAs across the chloroplast membrane. The same may be true for certain chloroplast proteins.
|
|
|
Some researchers have suggested that natural selection might act to keep certain genes in the plastid genome if their products are required to "lock in" or promote the accumulation of certain other proteins originally synthesized in the cytoplasm. This might apply in particular to multi component protein complexes composed of chloroplast and nuclear coded proteins is, such as the enzyme ribulose bisphosphate carboxylase (Rubisco), the chloroplast ribosomes, the ATP synthase and cytochrome b6/f complexes, and both the photosynthetic reaction centres.
|
A related hypothesis suggests that chloroplast coded proteins might be important in regulating the level of such multicomponent complexes. This would ensure that control of plastid functions remains in the plastid genome, which would help to explain the remarkable fact that so many multisubunit complexes include components by both chloroplast and nuclear genes.
Although we do not yet have much data on chloroplast DNA in chromophytic and rhodophytic algae, it is clear that these genomes do encode a number of the same genes found in the higher plant chloroplasts. In some cases they have also been shown to contain genes not present in the plastid genomes of higher plants.
One particularly interesting example is the presence of rbcS, the gene for the small subunit or Rubisco, on the chloroplast genome of algae of Cyanophora and Olisthodiscus. In both cases the rbcS gene is tightly linked to rbcL, the large subunit gene, and the two genes may be transcribed onto one RNA. Another example involves the phycobilisomes, complex light harvesting structures present in cyanobacteria and certain nongreen algae.
Genes for several phycobilisome proteins are encoded in the plastid DNA in Cyanophora.
Far more extensive alterations in the plastid genome have occurred during the evolution of another group of legumes the pea, broad bean, and clove group. Interestingly, this group consists of species whose chloroplast DNA does not contain the large inverted repeat found in all other higher plants and green algae.
It appears that loss of the inverted repeat occurred early in the evolution of this particular lineage and may have somehow led to an increase in the frequency of rearrangements in subsequent evolution.
Although the details of this evolutionary process are not understood, the extensive rearrangements in the genomes of pea, broad bean, and clove contrast strikingly with the very high degree of conservation seen in essentially all other vascular plant chloroplast genomes.
| |
