certain glutamate receptor subunit proteins (GluR-B) contain the amino acid arginine at a position where
the genomic DNA specifies a glutamine codon. The positively charged arginine residue in this protein is
essential for proper calcium transport in neuronal tissues and its incorporation was found to result from a
transversional RNA editing event. In the case of GluR-B, a specific glutamine codon (CAG) is converted
into an arginine codon (CIG) through an A→→I editing event that is catalyzed by the enzymes ADAR1 and
ADAR2 (Figure 7.23). It is now known that A→I editing in human tissues is extensive and its catalyzed
by a large family of specific ADAR enzymes.^42
7.2.3.2 Insertional and Deletional Editing. The most radical mRNA editing events occur in the
mitochondria of trypanosomatids, which are a group of parasitic unicellular eukaryotes. In these organisms,
long stretches of uridine are inserted into mRNA, and small numbers of encoded uridines are also removed.^44
The mitochondrial transcript doubles in length! This insertion–deletion editing is catalyzed by a set of
endonucleases and ligases that are targeted by specialized guide RNA molecules (gRNAs), which encode
the edited sequence. Whilst not as extensive as trypanosomatid editing, certain mRNAs from plants and
slime moulds have also been observed to undergo limited insertion, deletion, and even transversional editing.
The discovery of RNA editing in almost every type of organism serves as a cautionary tale in the current
age of whole-genome sequencing. Thus knowledge of genomic DNA sequence does not necessarily result
in accurate information about the sequence of the RNA and protein products.
7.2.4 Modified Nucleotides Increase the Diversity of RNA Functional Groups
7.2.4.1 Major Base Modifications in Mesophiles and Thermophiles. The information content of
nucleic acids is often further diversified by the post-transcriptional attachment of modifications, which
range in complexity from a simple methyl group to an entire amino acid or isoprenyl moiety. These modi-
fications, which are particularly common in “working RNAs” such as tRNAs and rRNAs, are attached to
RNA by a large family of modifying enzymes that are guided to specific target spots by various mechanisms.
DNA is frequently modified at the C-5-position of cytosine and the N-6 position of adenine. Base modifi-
cations provide a signal for gene silencing and, in higher eukaryotes, the cytosines in DNA are often more
likely to be methylated than not (Figure 7.24). However, the greatest diversity of modifications is found in
RNA molecules that are components of large cellular machines such as the ribosome and the spliceosome.
Modifications on both base and sugar moieties are common, particularly in thermophiles and hyperther-
mophiles, where they are believed to enhance the stability of RNA secondary and tertiary structure.^45
Depending on the functional group, nucleotide modifications can radically alter the chemical properties of
an RNA molecule, changing electrostatics, hydration, metal-ion binding, molecular recognition, and even
the redox properties (Figure 7.24).
7.2.4.2 Base Modifications in tRNA and rRNA. tRNA molecules contain numerous modifications,
which are involved in diversifying the genetic code, synthetase recognition, and stabilizing tRNA struc-
ture.^46 This is exemplified by the remarkable story of lysidine, which is a cytidine that has been post-
transcriptionally modified at the C-2 position with a lysine amino acid (Figure 7.24). In E. coli, isoleucyl
tRNA is only recognized and charged by its cognate synthetase enzyme when a lysidine base is present in
the tRNA anticodon loop. If lysidine is replaced by cytidine, the tRNA is mis-charged with methionine.^47
Thus, RNA modifications often blur the distinction between nucleic acid and protein, and they contribute
in fundamental ways to basic metabolism.
rRNA is heavily modified, particularly in regions that are conserved and critical for function (such as
the peptidyl transferase site). In mesophilic eukaryotic ribosomes, certain types of modification are par-
ticularly important. For example, a vertebrate ribosome is likely to contain 100 pseudouridineresidues
(Figure 7.24), which appear to be the dominant form of base modification in mesophilic organisms. Backbone
modifications are also observed, particularly in the form of abundant 2 -O-methyl groups(also 100
in vertebrate ribosomes). Modifications are placed at specific positions through a remarkable process that
RNA Structure and Function 271