Plant Genome Organization and Structure : RNA Editing

Analysis of Genomes by Reassociation Experiments

Repeated Sequences

Organization of Single-copy Sequences

Evolution of Repeated Sequences in Cereals

Estimating the Number of Expressed Genes

Chloroplast Genome Organization

Mitochondrial Genome Organization

RNA Editing

Course Topics

Course Home Page

RNA Editing

The Central Dogma of Molecular Genetics states that the information that is found in DNA is used to produce mRNA molecules that are instrumental in the production of proteins. Therefore, the information flows directly from DNA to protein, via the RNA intermediate molecule. Recently it has been discovered that the information that is contained in the DNA is not always found in the RNA products used to make proteins.

It has now been demonstrated that mitochondria and chloroplast contain the biochemcial machinery to alter the sequence of the final transcription product. This process is called RNA editing. This process was identified in the following manner. Sequence analysis of a number of cytochrome c oxidase subunit II genes from non-plant species revealed that a tryptophan residue was invariant at several locations in the final protein product. But sequence analysis of this gene in several plant species revealed arginine at those positions. This amino acid change would cause a radical alteration in protein structure because an acidic amino acid would replace a neutral, hydrophobic amino acid.

Position 1


Position 2


Since a single base pair change in the codons for the two amino acids could generate this change (CGG for UGG), it was suggested that CGG encoded for tryptophan and not arginine in plant mitochondria. (This is the only change in codon usage that has been suggested for plants and has been postulated for several other genes as well.) But this change in codon usage was not universal, that is some CGG codons actually specified arginine in the final protein product. Furthermore, no amino acyl tRNA that recognized CGG was found to be charged with tryptophan, a prerequisite if this codon specification was actually real.

The solution to this dilemma was found by sequencing the mRNA products for cytochrome oxidase subunit II genes. It was found that in the mRNA the cytosine residue had been changed (edited) to uridine at the sequence location where the invariant tryptophan residue is found. This changed the codon at that location to UGG which is recognized by a tRNA that carries the amino acid tryptophan. An analysis of three other plant mitochondrial genes where the same altered codon usage was predicted suggested that mRNA editing was also occurring at the codon and that a cytosine residue was edited to uridine. This editing process has also been detected in protozoa and it remains to be determined if RNA editing is a widespread function in mitochondria. A final point that this editing function highlights is that the sequence that is found in the DNA is not entirely and faithfully represented in the final protein product.

Specific Features of RNA Editing

  1. Editing can occur in both mitochondria and chlorplasts
  2. To date, >300 different editing events have been detected in plant mitochondria.
  3. The vast majority of the events involve a C to U tansition. A few cases of U to C transitions have been reported. This suggests that the editing machnery can also carry out the reverse modification.
  4. RNA editing can modify from 0.8% to 5.8% of the nucleotides of a specific transcript.
  5. The RNA editing events appear to occur at random in the transcript.
  6. Both 5' and 3' non-coding regions of mRNAs have also been shown to be edited.
  7. Structural RNAs such as tRNAs and rRNAs do appear to be affeceted.
  8. Editing can convert a tryptophan codon to a arginine codon (CGG to UGG).
  9. Start AUG codons can be created from ACG threonine codons
  10. Stop codons can be created by editing CAG, CAA and CGA codons.
  11. The most frequent amino acid substitions derived from RNA editing are Pro to Leu, Ser to Leu and Ser to Phe.
  12. Plant mitochondria do not use the universal genetic code.
The primary benefit of RNA editing could be evolutionary conservation of protein structure. For example, bound copper is required for the funciton of cytochrome c oxidase subunit II (coxII). After editing, all amino acids #228 are converted to cysteine, an amino acid required for copper to bind. In all species except for plants, the coxII gene encodes for methionine at codon #235. In plants, this methionine is generated by RNA editing. These events suggest that this protein is under very strong structural and functional constraints.

Copyright © 1998. Phillip McClean