Processing of rRNA and

tRNA

Subject - [Link] Botany, (Sem-III)

Paper - MBOTCC – 11, Unit – 3

Topic - Processing of rRNA and

tRNA

Dr. Punam Ranjan

Assistant Professor
Department of Botany
Patna Science College, Patna.
e-mail gayatripunam@[Link]
Introduction
• Posttranscriptional processing is not limited
to mRNA.
• Ribosomal RNAs of bacterial, archaeal, and
eukaryotic cells are made from longer
precursors called preribosomal RNAs, or pre-
rRNAs.
• Transfer RNAs are similarly derived from
longer precursors.
• These RNAs may also contain a variety of
modified nucleosides; some examples are
shown below.

Source- Lehninger Principles of Biochemistry; Nelson and Cox, 6th edition

Figure- Some modified bases of rRNAs and
tRNAs, produced in posttranscriptional
reactions. The standard symbols are shown in
parentheses. Note the unusual ribose
attachment point in pseudouridine. This is just a
small sampling of the 96 modified nucleosides
known to occur in different RNA species, with
81 different types known in tRNAs and 30
observed to date in rRNAs (approx data). For
current detail see RNA database.

rRNA Processing
Ribosomal RNAs In bacteria, 16S, 23S, and 5S
rRNAs (and some tRNAs, although most tRNAs
are encoded from other places) arise from a
single 30S RNA precursor of about 6,500
nucleotides. RNA at both ends of the 30S
precursor and segments between the rRNAs
are removed during processing.
 Source- Lehninger Principles of Biochemistry; Nelson and Cox, 6th edition

Figure- Processing of pre-rRNA transcripts in bacteria.

1- Before cleavage, the 30S RNA precursor is methylated at specific bases (red
tick marks), and some uridine residues are converted to pseudouridine (blue
tick marks) or dihydrouridine (black tick mark) residues. The methylation
reactions are of multiple types, some occurring on bases and some on 2’-
hydroxyl groups.
2- Cleavage liberates precursors of rRNAs and tRNA(s). Cleavage at the points
labeled 1, 2, and 3 is carried out by the enzymes RNase III, RNase P, and
RNase E, respectively. RNase P is a ribozyme.
3- The final 16S, 23S, and 5S rRNA products result from the action of a variety
of specific nucleases. The seven copies of the gene for pre-rRNA in the E. coli
chromosome differ in the number, location, and identity of tRNAs included in
the primary transcript. Some copies of the gene have additional tRNA gene
segments between the 16S and 23S rRNA segments and at the far 3’ end of
the primary transcript.
The 16S and 23S rRNAs contain modified nucleosides. In
E. coli, the 11 modifications in the 16S rRNA include a
pseudouridine and 10 nucleosides methylated on the
base or the 2-hydroxyl group, or both.
The 23S rRNA has 10 pseudouridines, 1 dihydrouridine,
and 12 methylated nucleosides. In bacteria, each
modification is generally catalyzed by a distinct enzyme.
Methylation reactions use S-adenosylmethionine as
cofactor. No cofactor is required for pseudouridine
formation.
• The genome of E. coli encodes seven pre-rRNA
molecules. All of these genes have essentially identical
rRNA-coding regions, but they differ in the segments
between these regions.
• The segment between the 16S and 23S rRNA genes
generally encodes one or two tRNAs, with different
tRNAs produced from differen pre-rRNA transcripts.
• Coding sequences for tRNAs are also found on the 3’
side of the 5S rRNA in some precursor transcripts.

The situation in eukaryotes is more complicated. A 45S

pre-rRNA transcript is synthesized by RNA polymerase I
and processed in the nucleolus to form the 18S, 28S,
and 5.8S rRNAs characteristic of eukaryotic ribosomes.
There is a tight coupling between rRNA transcription,
rRNA maturation, and ribosome assembly in the
nucleolus. Each complex includes the ribonucleases that
cleave the rRNA precursor, the enzymes that modify
particular bases, large numbers of small nucleolar RNAs,
or snoRNAs, that guide nucleoside modification and
some cleavage reactions, and ribosomal proteins.
Source- Lehninger Principles of Biochemistry; Nelson and Cox, 6th edition
Figure- Processing of pre-rRNA transcripts in vertebrates.
During transcription, the 45S primary transcript is
incorporated into a nucleolar 90S preribosomal complex,
in which rRNA processing and ribosome assembly are
tightly coupled.
1- The 45S precursor is methylated at more than 100 of
its 14,000 nucleotides, either on the bases or on the 2’-
OH groups, some uridines are converted to
pseudouridine, and a few other modifications occur.
2- A series of enzymatic cleavages of the 45S precursor
produces the 18S, 5.8S, and 28S rRNAs, and the ribosomal
subunits gradually take shape with the assembling
ribosomal proteins. The cleavage reactions and all of the
modifications require small nucleolar RNAs (snoRNAs)
found in protein complexes (snoRNPs) in the nucleolus
that are reminiscent of spliceosomes. The 5S rRNA is
produced separately.
• The most common nucleoside modifications in
eukaryotic rRNAs are, again, conversion of uridine to
pseudouridine and adoMet-dependent nucleoside
methylation (often at 2’-hydroxyl groups).
• These reactions rely on snoRNA-protein complexes, or
snoRNPs, each consisting of a snoRNA and four or five
proteins, which include the enzyme that carries out
the modification.
• There are two classes of snoRNPs, both defined by key
conserved sequence elements referred to as lettered
boxes. The box H/ACA snoRNPs are involved in
pseudouridylylation, and box C/D snoRNPs function in
2’-O-methylations.
• Unlike the situation in bacteria, the same enzyme may
participate in modifications at many sites, guided by
the snoRNAs.
• The snRNAs and snoRNAs not only facilitate RNA
processing reactions but are themselves synthesized
as larger precursors, and then processed.
tRNA processing
• Transfer RNAs Most cells have 40 to 50 distinct tRNAs,
and eukaryotic cells have multiple copies of many of
the tRNA genes. Transfer RNAs are derived from longer
RNA precursors by enzymatic removal of nucleotides
from the 5’ and 3’ ends.
• In eukaryotes, introns are present in a few tRNA
transcripts and must be excised. Where two or more
different tRNAs are contained in a single primary
transcript, they are separated by enzymatic cleavage.
The endonuclease RNase P, found in all organisms,
removes RNA at the 5’ end of tRNAs.
• This enzyme contains both protein and RNA. The RNA
component is essential for activity, and in bacterial cells
it can carry out its processing function with precision
even without the protein component. RNase P is
therefore another example of a catalytic RNA, as
described in more detail below. The 3’ end of tRNAs is
processed by one or more nucleases, including the
exonuclease RNase D.
• Transfer RNA precursors may undergo further
posttranscriptional processing. The 3-terminal
trinucleotide CCA(3’) to which an amino acid is
attachedduring protein synthesis is absent from some
bacterial and all eukaryotic tRNA precursors and is
added during processing.
• This addition is carried out by tRNA
nucleotidyltransferase, an unusual enzyme that binds
the three ribonucleoside triphosphate precursors in
separate active sites and catalyzes formation of the
phosphodiester bonds to produce the CCA(3’)
sequence. The creation of this defined sequence of
nucleotides is there fore not dependent on a DNA or
RNA template—the template is the binding site of the
enzyme.
• The final type of tRNA processing is the modification
of some bases by methylation, deamination, or
reduction. In the case of pseudouridine, the base
(uracil) is removed and reattached to the sugar
through C-5’. Some of these modified bases occur at
characteristic positions in all tRNAs.
 Source- Lehninger Principles of Biochemistry; Nelson and Cox, 6th edition

Figure- Processing of tRNAs in bacteria and eukaryotes.

The yeast tRNATyr (the tRNA specific for tyrosine binding, is
used to illustrate the important steps.
The nucleotide sequences shown in yellow are removed
from the primary transcript. The ends are processed first,
the 5’ end before the 3’ end. CCA is then added to the 3’
end, a necessary step in processing eukaryotic tRNAs and
those bacterial tRNAs that lack this sequence in the
primary transcript.
While the ends are being processed, specific bases in the
rest of the transcript are modified. For the eukaryotic tRNA
shown here, the final step is splicing of the 14 nucleotide
intron. Introns are found in some eukaryotic tRNAs but not
in bacterial tRNAs.
SuggeSted Book and RefeRenceS
 LehningeR PRinciPLeS of BiochemiStRy;
neLSon and cox, 6th edition